I commented on the WR run on youtube with the question of can we use an emmulator and the moderator said yes. I would assume VBA and the like are run worthy based off of that. I would be using either VBA for windows or gpemu for chromebook if it was me.
VBA seems to vary in speed sometimes (99%-101%), so I'm not sure if it's the best option for a speedrun. Though I'd personally accept it as I wouldn't want to put unneccesary hurdles for someone looking to run the game.
Late to the party but if you want accuracy you want to be using mGBA. This emulator covers Windows, Linux and Mac operating systems.
I've updated the rules for the categories such that mGBA is the only current emulator. Older runs that have been submitted will be grandfathered in at their current position.