Technically, it all is alternate timelines. Like the remakes, 3rd versions, and reimagining's all take place in separate, but very similar timelines, and that's been the case for a while. The modern games played up to it, which gave reasonings as to why the remake and 3rd version games are different than the mainline dual versions. And really, the best, and really only, way to put it is that they're all just alternate timelines/dimensions, they just fleshed it out starting with Gen 7. When it comes to referencing back, they tend to use the 3rd versions as the definitive one.
Like some examples on this:
Emerald is the game that SuMo used when bringing back Anabel. Since Emerald never got a remake, the Battle Frontier wasn't a thing, and thus Anabel was missing, they had to give an explanation on how she came back, especially since it follows ORAS's timeline.
Platinum is the game Legends used when it came to being a prequel. All the Sinnoh backstory correlates to Platinum exclusive story.