Bitrate discrepancy of cleaned flac files

Reported privately:

Before use mat2:

ffprobe -i '01. Sing My Pleasure.flac'
ffprobe version 4.1.6-1~deb10u1 Copyright (c) 2007-2020 the FFmpeg developers
  built with gcc 8 (Debian 8.3.0-6)
  configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
  WARNING: library configuration mismatch
  avcodec     configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
--enable-version3 --disable-doc --disable-programs --enable-liblensfun
--enable-libopencore_amrnb --enable-libopencore_amrwb
--enable-libtesseract --enable-libvo_amrwbenc
  avfilter    configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
--enable-version3 --disable-doc --disable-programs --enable-liblensfun
--enable-libopencore_amrnb --enable-libopencore_amrwb
--enable-libtesseract --enable-libvo_amrwbenc
  libavutil      56. 22.100 / 56. 22.100
  libavcodec     58. 35.100 / 58. 35.100
  libavformat    58. 20.100 / 58. 20.100
  libavdevice    58.  5.100 / 58.  5.100
  libavfilter     7. 40.101 /  7. 40.101
  libavresample   4.  0.  0 /  4.  0.  0
  libswscale      5.  3.100 /  5.  3.100
  libswresample   3.  3.100 /  3.  3.100
  libpostproc    55.  3.100 / 55.  3.100
Input #0, flac, from '01. Sing My Pleasure.flac':
  Metadata:
    DATE            : 2021
    TOTALTRACKS     : 5
    track           : 1
    ALBUM           : Sing My Pleasure
    ARTIST          : ヴィヴィ(Vo.八木海莉)
    GENRE           : Anime
    TITLE           : Sing My Pleasure
  Duration: 00:04:49.27, start: 0.000000, bitrate: 1099 kb/s
    Stream #0:0: Audio: flac, 44100 Hz, stereo, s16
    Stream #0:1: Video: mjpeg, yuvj444p(pc, bt470bg/unknown/unknown),
700x700 [SAR 150:150 DAR 1:1], 90k tbr, 90k tbn, 90k tbc
    Metadata:
      comment         : Cover (front)

After use mat2:

ffprobe -i '01. Sing My Pleasure.cleaned.flac'
ffprobe version 4.1.6-1~deb10u1 Copyright (c) 2007-2020 the FFmpeg developers
  built with gcc 8 (Debian 8.3.0-6)
  configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
  WARNING: library configuration mismatch
  avcodec     configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
--enable-version3 --disable-doc --disable-programs --enable-liblensfun
--enable-libopencore_amrnb --enable-libopencore_amrwb
--enable-libtesseract --enable-libvo_amrwbenc
  avfilter    configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
--enable-version3 --disable-doc --disable-programs --enable-liblensfun
--enable-libopencore_amrnb --enable-libopencore_amrwb
--enable-libtesseract --enable-libvo_amrwbenc
  libavutil      56. 22.100 / 56. 22.100
  libavcodec     58. 35.100 / 58. 35.100
  libavformat    58. 20.100 / 58. 20.100
  libavdevice    58.  5.100 / 58.  5.100
  libavfilter     7. 40.101 /  7. 40.101
  libavresample   4.  0.  0 /  4.  0.  0
  libswscale      5.  3.100 /  5.  3.100
  libswresample   3.  3.100 /  3.  3.100
  libpostproc    55.  3.100 / 55.  3.100
Input #0, flac, from '01. Sing My Pleasure.cleaned.flac':
  Duration: 00:04:49.27, start: 0.000000, bitrate: 1097 kb/s
    Stream #0:0: Audio: flac, 44100 Hz, stereo, s16

After use mat2 -L:

ffprobe -i '01. Sing My Pleasure.cleaned.flac'
ffprobe version 4.1.6-1~deb10u1 Copyright (c) 2007-2020 the FFmpeg developers
  built with gcc 8 (Debian 8.3.0-6)
  configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
  WARNING: library configuration mismatch
  avcodec     configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
--enable-version3 --disable-doc --disable-programs --enable-liblensfun
--enable-libopencore_amrnb --enable-libopencore_amrwb
--enable-libtesseract --enable-libvo_amrwbenc
  avfilter    configuration: --prefix=/usr --extra-version='1~deb10u1'
--toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu
--incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl
--disable-stripping --enable-avresample --disable-filter=resample
--enable-avisynth --enable-gnutls --enable-ladspa --enable-libaom
--enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca
--enable-libcdio --enable-libcodec2 --enable-libflite
--enable-libfontconfig --enable-libfreetype --enable-libfribidi
--enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame
--enable-libmysofa --enable-libopenjpeg --enable-libopenmpt
--enable-libopus --enable-libpulse --enable-librsvg
--enable-librubberband --enable-libshine --enable-libsnappy
--enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora
--enable-libtwolame --enable-libvidstab --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265
--enable-libxml2 --enable-libxvid --enable-libzmq --enable-libzvbi
--enable-lv2 --enable-omx --enable-openal --enable-opengl
--enable-sdl2 --enable-libdc1394 --enable-libdrm --enable-libiec61883
--enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
--enable-version3 --disable-doc --disable-programs --enable-liblensfun
--enable-libopencore_amrnb --enable-libopencore_amrwb
--enable-libtesseract --enable-libvo_amrwbenc
  libavutil      56. 22.100 / 56. 22.100
  libavcodec     58. 35.100 / 58. 35.100
  libavformat    58. 20.100 / 58. 20.100
  libavdevice    58.  5.100 / 58.  5.100
  libavfilter     7. 40.101 /  7. 40.101
  libavresample   4.  0.  0 /  4.  0.  0
  libswscale      5.  3.100 /  5.  3.100
  libswresample   3.  3.100 /  3.  3.100
  libpostproc    55.  3.100 / 55.  3.100
Input #0, flac, from '01. Sing My Pleasure.cleaned.flac':
  Duration: 00:04:49.27, start: 0.000000, bitrate: 1097 kb/s
    Stream #0:0: Audio: flac, 44100 Hz, stereo, s16

In this case only down 2 kb/s, I have a lost of 20 kb/s in other cases.

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Bitrate discrepancy of cleaned flac files

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