It gives a placement in time. Bill and Lanette made thiers together. As far as we know it could have been made right before you started your journey as they were still tweeking it. Same with Bebe's and Amnita's PCs.
It's not as much about world domination as it is about being noticeable, as mentioned when the Plasma Grunt says Rocket and Galactic had 'drawn too much attention to themselves'. So you're saying that Magma and Aqua's actions didn't draw quite the attention to themselves? I really disagree there.
Yes reason for it is opinion based and I posted MY opinions. No Aqua and Magma weren't really out there with their plots. Only a few times to small amounts of people. They didn't do anything of merit through the original main games (R/S) with the largest possible being the awakenings which probably went unknown as not all of Hoenn was effected, nor do the people know who awakened them. Largest for the Director's Cut (E) was the space station attack. But with split universes we can't say what is Canon for sure as based on HG/SS Events in Emerald were not Canon, but if you don't include remakes then either could be Canon.
Gens 3 and 4 are the only ones with parallel worlds with drastic dynamic changes to the story unlike all past and current games.
Parallels to all the Initial Duo games are always even, and the first two thirds didn't change much with the main story while Gens 3 and 4 game second tellings of the stories with a heavy change to the overall plot to include both original Legends Plus one.