The "normal" 616 universe is still under a crazy-Wanda mass delusion like in House of M. It's just that the main mass delusion is centered around "No More Mutants," and in this world Tony Stark has been almost completely junked as a character, Spider-man is no longer married to Mary Jane, SHIELD has been dissolved and Norman Osborn in charge of US security, and a whole bunch of other recent Marvel weirdness. It seems minor, then, that another part of the delusion is Wanda's children still being around.
However, if the characters in 616 realize they're still being deluded, and reverse the universe, sure a bunch of bad editorial and story decisions get reversed along with it . . . but so do some good things.