FLAC files can have ID3 tags. Though it is recommended only to use FLAC type tags (like Vorbis Comment), some people use those.
I think it would be good to introduce an additional section in Tools/Options/Tags to handle FLAC files separately: So one could more easily specify which kind of tags should be read/written/removed.
(Just got a FLAC file that was ID3v2 tagged, added ReplayGain using metaflac and found I could suddenly only see the FLAC tags generated by metaflac. So I had no chance to specify something like »read both FLAC+ID3v2, write FLAC, remove everything except FLAC«.)
This would be especially neat since I currently use Mp3tag and a batch Export to replay-gain my whole collection (which replay-gains album-oriented, auto-distinguishing between MP3, OGG, and FLAC). It would be great if I could go through all FLAC files before and re-tag those to FLAC tags only that might be mis-tagged using ID3v2.