The tags in the example (m4a) don’t seem wrong, they are read correctly by picard, kid3, ffmpeg, feishin, tempus, and audacious. Neither does anything seem incorrect while looking at the metadata in a hex editor.
For the rest of the non-flac tracks, replay gain seems to be applied in the logs, but is not audible during playback, causing them to play much louder.
Could this be something device specific? I am using a Pixel 9 with GrapheneOS.