It's certainly possible, but Mewtwo is the only one that anyone ever says there is only one of. As for the others, I used to think only the deities like Arceus, Palkia, Dialga and Giratina were the truly unique ones, but now it seems not even the creation trio are sacred when it comes to churning out multiples. Some legendaries are completely canonically non-unique. Like Latias and Latios living in herds. But basically seeing as Mewtwo is "Legendary" when he is brand new (so not even "there are legends about them" can be used as a definition), I think it's basically just that they're rare.
Anyway, to curb this back towards the topic, I don't think the new universe deal has anything to do with how many legendaries they put in ORAS, or the different locations legendaries are found in. They can move or there are multiples, it really doesn't matter a whole lot. The reason is basically just to retcon Mega Evolution. Anything with megas is one universe, anything without is not that universe (and there maybe multiples there, such as between game versions). By that definition all we know for certain to be in the Mega Universe is XY, ORAS, and Pokemon Origins. The main anime is all over the place with canon and non-canon, so it may be best to leave it to its own thing.