>>24639518Possibly confirmed in ORAS...
Ruby and Saphire were the last games chronologically. The weather catastrophe is never directly referenced in any other game, even though other events are mentioned.
This is significant thanks to the Meteorite scare in Delta Episode. Though we never play through the scenario in RSE, there's nothing saying it doesn't happen at some point in that timeline.
Without Mega Fug to destroy the meteor, the backup plan, using teleporters, has to be used. This means that the warp rocket plan was put into effect in RSE timelines, leading to meteors getting thrown into other universes without warning.
Without Fug, Praise the Sun, and Superfish, free and able to remake the world after the catastrophe, it falls upon another group of legendaries to remake the world after the meteor lands.
The reason we see rifts in time and space in Hoenn (Those not caused by Hoopa), is because the warring gods haven't quite had enough time to settle down and smooth things out in the new timeline/multiverse branches.