A legendary don't have to be unique.
Entei's Pokedex entry says that each time a volcano erupts, a new Entei is born.
Latias' travel in herd.
There are a lot of Mews too.
You can create more Giratinas, Palkias, and Dialgas as long as Arceus exists - Like how you can create more in HGSS, perhaps Arceus create more, or most probably clone itself into more Arceuses too.
Entei's Pokedex entry says that each time a volcano erupts, a new Entei is born.
Latias' travel in herd.
There are a lot of Mews too.
You can create more Giratinas, Palkias, and Dialgas as long as Arceus exists - Like how you can create more in HGSS, perhaps Arceus create more, or most probably clone itself into more Arceuses too.