Correct me if I'm wrong but, as far as I know, asumming the Pokémon series follows a story line and all the games are not in separate universes, there is a truly bit number of unique legendaries. Pokémon like the regis, Cresselia, Heatran, the bird trio, the legendary beasts, lati twins... are used by a large amount of trainers in places like the Battle Frontier, implying they are not unique. What is more, most of them can be found in different locations, in different generations, in different regions. Even the rarest of the Pokémon, say Ho-Oh or Lugia, can be found in different places (talking about the main series not spin offs): navel rock, tin/bell tower, sea mauville (welp, in this case the Pokémon is teleported from another location so ill give it the benefit of the doubt).
I think Game Freak has never pronounced about which legendaries are truly unique at this moment.