Not completely sure how I feel about ORAS and RSE seemingly being two different parallel universes that split depending on the actions 3000 years ago. I don't think ORAS overriding RSE would have caused more problems than alternative timelines. It just seems a bit too weird, even in-universe.
I'm kinda hoping it's just some kind of metaphor or something; it raises so many unanswered questions and ruins some canon things I think...not completely sure...