The habitats might be huge, but it's still very limiting in its own way. Take Jubilee and Shogo for example;
Shogo is only a baby. Jubilee, meanwhile, might be especially excited to finally be able to celebrate just being herself--to go out and enjoy all Krakoa has to offer...! Except...she has an infant son. And no, she can't just always leave him with a babysitter, because outside of availability of one...she can't enjoy what's there without her baby. As he grows, the family attractions will forever be off limits to him, he won't get to go and make a wider variety of friends, he won't understand the joy of mutant culture to its' fullest extent. All he'll know is that he's only allowed on the outskirts. And, yes, being a human he might never truly 'get' what makes it so special and wonderful, but cutting him off from a big part of his family's life isn't going to help.
Same with other mutant parents who might yet have a human child. Say someone has twins; one's a mutant, one's a human--there's a festival or something going on at the mainland...either both parents leave one kid behind and go and have just the best day ever (as their sibling might very well describe it) without them, or nobody goes at all, ever?