I'm sorry, but that is how I see the argument. Complaining if they do a mainly female X-Men because %'s should work that way, when the world population is almost 50/50 men vs women, so if %'s were to be followed, it should apply not just to mutants, but enhanced as well. Many of the most iconic female characters are mutants, so it is the most sensible place to mine. You can't have it both ways.
Rationally, it's not the same. There are lots of different origin stories for superpowers, and they don't all logically entail sex parity. Like, most soldiers are male, so if Super Soldiers/sci-fi military equipment is one of several possible origins, the laws of genetics don't have to warp so that extra female babies are born with the X-gene to balance out male enhanced soldiers.
If there's a rational idea for getting women to outnumber men, that's fine, but implying that I shouldn't apply reason to a superhero universe or it's internalized misogyny is pure postmodernism.