While it's tempting to think this is an OFFICIAL RETURN, bear in mind that BOOM! is not Disney, we're just a licensee. Disney still retain the right to do whatever they want with the characters and they certainly don't have to take anything WE do in the comics as official canon unless they want to.
So until someone from Disney proper officially states 'Skeeter is legitimately part of current Muppet canon', just take our comic story as a very lucky, fortunate diversion for Muppet lovers.
What happens after this is wide open.
I see what you mean and I agree... but it is an official product featuring her return, which I mean as opposed to another fan fiction. The fact that there is some supervision from the main company that allowed it (again, they could have refused) makes a it real nod to us fans who actually wanted this to happen in some form of media, be it just a comic book. Now, I don't consider the comic book part of "canon," but if you look hard enough, I don't think there was ever any attempt at an official canon at all. The Muppet Movie says one thing, The Muppet Show says another, Muppet Babies implies something completely different, and it was a fantasy sequence in another movie that says something else completely different. And the fact they reference MB in Muppet Family Christmas adds to confusion.
Even in a comic book, I wouldn't count Skeeter as canon... again, it implies Muppet Babies is part of it, but it is canon in the sense that the comic book is it's own little world. So it's an official piece of media that features an adult her, just not an official part of Muppet Canon... whatever one would actually be.