Gods, going to test my knowledge, but I think she's bounced back and forth between being mutant or not for a while. And I don't know what her current backstory is in the comics. I know she's in a weird area of being more associated with the Avengers, but technically a mutant. Which is why she can appear in both universes.
Though just by looking at the MCU and Fox-Men, there may have been an under the table agreement to split the children between studios.