>>17388926They've acknowledged that many legendaries aren't unique before, both in game, and through other media. (Multiple Darkrai, Lati@s, Mewtwo's, Lugia's, ect. in the Anime!-verse)
And in terms of actually catching legends, Hilda/Hilbert and Serena/Calem are the only characters who as part of the plot, actually catch their legendaries. Rosa/Nate also own N's Zekrom/Reshiram if that matters.
If you accept the Headcanon that every Protagonist completed their own Regional Dex, then you could stretch it and say that there are, for example, 3 known Mewtwos in the Game-verse, but outside of GF acknowledging Red catching them all in Origins, there's no proof of that.
If we do accept that Red did catch a Mewtwo, and the birds, then we can accept that there are at least two Mewtwo's, and multiple birds.
But again, this is all headcanon territory. Truth is, nobody knows how many of each legendary Pokemon there are, and Zekrom/Reshiram/Xerneus and Yveltal are the only ones acknowledged to have been caught in game.