Prof. SALTY
The Scruffy Professor
This timeline stuff that's been going on since ORAS is honestly really pointless. Pokemon is constantly contradicting itself with each new installment, so I have no idea why people keep trying to categorize it into two timelines.
Multiverse theory states that there are an infinite number of parallel universes. An infinite number of different scenarios. Heck, you could argue that each individual game people buy is its own separate timeline. They're all very similar, but things (like Pokemon teams and whatnot) aren't always the same.
...This does bring in the question what happens to said timelines when you delete your save, but that's a discussion for another day.
You're confusing timelines and universes. ORAS did imply that each game is a different universe, but there are only 2 speculated timelines. I'm bad at analogies so I won't butcher the English language trying but multiple universes can fit in a timeline but only one timeline can contain a universe... if that makes sense.
Of course Game freak don't give a hoot about timelines anyway really. They confirmed where roughly everything lies in the OG timeline but they dont seem to care about the (dubious) mega timeline.