I think this has been touched upon before. I'm not sure if it's actually been requested, though.
EAC, an extremely popular ripping program, for whatever reason, can easily be configured to add ID3v2 tags to files that it externally encodes in Flac (and perhaps to other file formats as well). This leads to a lot of Flac files that contain ID3v2 tags.
Yes, you're right, they shouldn't be there. Yes, it's an application problem or a user configuration error.
Nonetheless, they exist. And a good tagging tool to remove these tags does not exist.
Please apply the 'Remove Tag' settings (better yet, create new settings for Flac) to Flac files so that nobody has to go through the Ctrl-R, Ctrl-Z method of removing tags. Typically, this operation would be applied to an entire library and there are far too many things that can go wrong using this procedure that removes all tags from Flac files.
One other very dangerous issue regarding Remove Tags an Flac files is that if someone has a mixed format library and loads both Mp3 and Flac files into Mp3tag, then performs a 'Remove Tags' operation, they will remove all of the Flac tags from their files. Usually, that's not what they'll want.