I have some M4A files that have encoder version information (string like Lavf57.41.100) from FFmpeg, and these don't show up in MP3Tag, and this seems to prevent the "MP4" tag from being removed fully.
There are M4A files which do not contain this field, and can actually have the MP4 tags removed fully in Mp3tag. So I think it could be fixed.
This came up because I was trying to find duplicate files, but the fact that two M4A files are the same but with a different encoder version meant that they were hashed differently. I was hoping that Mp3tag could fully remove the tags so the duplicates could be removed, but this was not possible.
Only solution ended up being reprocessing all files losslessly in FFmpeg so that the version string is the same across all files, which is not ideal because FFmpeg does not support overwriting files.
Thank you, hope this report makes sense.