Mp3tag reads tags into a common GUI, so if the fields it reads are different it could give a warning. Length is no problem--just compare up to the length of the shorter field. I don't want to deal with APE tags, because the other tools I use normally don't write them. I've yet to encounter an MP3 file that has had ONLY the APE tag. If I see no tag information at all, the first thing I'll look for is the info in %_tag% displayed in parentheses in the default TAG field. If I ever see only APE, I'll read it and write ID3v2.3 UTF-16.
Did you see Post #17 - this might bring you further than the discussion about the different perception of tag versions.