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Giving the opportunity for the player to catch legendary and mythical pokemons for completeness sake or as rewards doesn't necessarily imply that a pokemon is not unique.
Also you could argue that a legendary/mythical pokemon moves around between regions.
Only the game's lore can tell ou if a pokemon is certain or implied to be unique.
The Eon duo for example are explicitly said to just be part of a really rare species in the pokedex, even though they're unique in the games.
