Their powers are specific traits to them, it doesn't detract them from being humans. There are various branches of humanity in 616, if the mutants want to consider themselves as non-human beings, they can, absolutely. That doesn't make it biologically true though.
I don't see what culture and society have anything to do with what is biological in nature. Sapiens and mutants are two sides of the same coin that is humanity. It's that simple.
It's akin to you saying Neenderthals weren't humans, but Sapiens were. No. They were both humans, each kind with specific traits, that's the exact same thing with Sapiens and Mutants.