X-men has never had one unified canon. There was one canon for the comic books, one for the, TV show, and an entirely different one for the movies. The characters and events are basically the smae, but what order they happen in and who's involved in them, and even who's a good guy and whose a bad guy, changes with each incarnation.
This will be both a blessing and a curse as far as Mutants! the Musical is concerned. On the one hand, it can have it's own canon, designed to incorporate the maximum number of mutant song and dance numbers. On the other hand, a lot more writing will be involved.