Late reply,

but short answer is no, when you start an Any% run (or a 100% run for the matter) it has to be on a clean file, your timer should start when you select your clean file and start your game

I'm not a mod here so it's just my opinion, but it's not like speedruning this game is competitive or anything so you should be free to play on whatever software you want. You should just write it down below your run that you played on xboxAdvance I'm always happy to see more runners of this game so welcome !