Mmm true, though presumably if you keep the Textures externally from the ROM itself, it might be possible to have say a Textures subfolder for an emulator, and within that folder would be folders relating to certain ROMs.
(Eg Textures
> MarioWorld > MarioKart etc)
Then you could place here the replacement textures, and a .TXT file to say which hex positions the BMPs relate to?
This is all very broad, I'm coming at this from a Quake/HL2 modding perspective.