Probably. But fundamentally, the mutants don't need the wider Marvel Universe for any part of their worldbuilding. They would be hated and feared because they represent organic natural evolution over man's need to dominate and harvest and leech off the environment for its own advancement.
The arrival of the mutants could lead SHIELD and others to ally and cool down with the super-powered folks. Call it a truce and old enemies ally against a new threat a bit like how waves of immigrant groups get co-opted by WASPs to persecute the waves that come after them.