Sure it does. It was never said that there was only ever one of any Legendary Pokémon aside from Mewtwo. In theory, there could be multiples of all of them, even the Creation Bunch.
HOWEVER, this multiverse concept does explain the differences between the GBA/DS era and the 3DS era (Mega Evolution having existed for all this time, Mewtwo being in Kalos instead of Kanto, etc.).
And anyway, it's really very simple actually. We just have two different continuities now, but it's not like we couldn't have already assumed that to be the case for the GB/GBC games in relation to the GBA/DS games. Now it's just:
Universe 1: RGB (and Yellow, I guess, if you're into that kind of thing) > GSC
Universe 2: FRLG/Emerald > HGSS/Platinum > BW > B2W2
Universe 3: ORAS > XY (Or is it the other way around? I don't have confirmation on this yet.)
I always thought that the Pixies left the lakes in DP (because of what Team Galactic did) and moved to Unova.
As for the Regis, I think there are actually supposed to be multiples of the trio and just one leader. The Regis in Hoenn also affect Kanto, the Regis (event) in Sinnoh also affect Johto and there's also a set in Unova. That way it's more like one per continent.
Oh and the reason why the
As for the universes, I'd say:
Universe 1: RGB ~ E-> GSC ~ DP -> BW -> B2W2
This is pretty much the prime/incomplete universe. Many things go unanswered.
Universe 2: Y -> HGSS -> Pt
Pokémon are more likely to follow you around. The reason for this, is because of the great example Red set in Yellow, by winning the league. There are also more Pokémon which follow you in that park area in Platinum. This is also considered to be a more expanded universe.
Universe 3: FRLG ~ RS ~ Colosseum -> XD
FRLG, RS and Colosseum all happen at about the same time. This universe is fairly self-contained.
Universe 4: XY -> ORAS
The "new" universe. Pokémon distribution is a lot more vast here than in other timelines.