The GBA version is actually Mother 2 since it's not in English and they coded it very differently from the original, so if we did accept it it would have to go under Any% Glitchless (JP) and even then we might have to separate it from the normal category since it's so different from the original Mother 2.
So long story short, no it's not allowed.
The other answer to the question is of course, you can run whatever game you want however you want to run it, but it might not be allowed on the EB leaderboards because it's fundamentally a different game.
Stuff like killing Giygas with poison, for instance, doesn't exist in the SNES version or its derivatives.
Which isn't to say that it's not (necessarily) worth running, but it'd be like running SM64 DS instead of the N64 version - it's its own game with its own leaderboards, rules, etc.
