RMM/RMML's Order of tag preference (last in list "wins") at import time:

MP3: ID3v1, ID3v2
Ogg: IdentificationHeader
FLAC:Ogg comments, ID3v2

In the case of MP3, I believe they are superimposed -- so ID3v1 gets read in, then ID3v2 is overlayed on top (and duplicates, ID3v2 wins). However, on FLAC, I think if there are ID3v2, it and only it gets used.

For uniqueness calculation:
MP3: After ID3v2 to before ID3v1
Ogg: Entire file
Flac: After ID3v2 to end of file

Other than that, they are treated equally (except obviouslly, the choice of codec for playback on the player)