Originally Posted by
Bovinity Divinity
The current WR for Mega Man X is a tie between an console run and an emulator run, so they seem to be accepted. Darn near every applicable game on the speedrun.com leaderboards has times from emulators, and SRL has them mentioned as legal for races. (As long as accepted by the community in general for a specific game)
So there might be issues, but they're not a no-no by any means. I'm sure if there are issues with any given game, the community for it knows the time differences anyway. (And they're likely smaller differences than using JP or EN carts, or PRG0/PRG1 carts in the case of some NES games.)