For the most part you can make good guesses but I'm loving the loose assumptions of RSE's place in the timeline.
Trading is next to no proof of a gen happening at the same time as another. You can also freely trade and battle between Black/White and Black 2/White 2, despite the latter games taking place two years later. Trading is just more of a way to retcon things and is more a game mechanic than a plot point.
Something else to note about is how Magma and Aqua had no mention in Black/White(despite their actions being far more noteworthy than Rocket) , yet they appeared in Black 2/White 2(as former members of course) and, imo, speak as if what they did wasn't that long ago. That shows that there is also a chance of the big events in RSE happening inbetween both sets of Gen 5 games. That could also explain Steven being champion in HGSS because neither us nor Wallace has probably beaten him yet. I'm sure we also aren't the only silent yet strong trainers around. There's a lot of ways to interpret what we do know.
It's pretty obvious that there were more Pokemon that existed outside of those areas. It's not like Kanto was the only region and the others just continuously popped up out of nowhere(we only know of the number of Pokemon as the regions are brought out and because I'm sure they don't have every Pokemon/region planned out already).
With that said, Hoenn and (all) other regions more than likely existed with their Pokemon before we visit them in the games. That, however, does not mean the big events(what we have to go through playing the games) happen together. There is pretty much nothing solid that gives Gen III a specific spot is what I'm saying.
Other than that, the others seem to have a better way to judge where they are.