Despite the fact that I do not have any of the 'Remove' check boxes checked, when I select File, Remove Tag it removes all tags from m4a files. It does not remove any ID3 tags from mp3s.
ID3 for MP4 is not supported by Mp3tag and the format itself, so if you have MP4 files with standard ID3 tags, the files are probably broken.
Did you mean "MP4s" instead of "MP3s" in your last sentence?
Sorry - that was a bit confusing.
With no tag types selected for removal, 'Remove' will clear the tags within an M4A file (MP4 tag) but will leave MP3 files (ID3 tags) alone.
Yes, this is intended.
MP4 files only can have MP4 tags, so there is no additional option needed.
What if I don't want the M4A tags removed? There's no option to not remove them.
If you don't want to have them removed you don't click on the red X. If you have lots of files of different formats, you can sort by codec and only select the files you want to edit.