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I know that not all legendaries are unique or one of a kind, but there are a few that are (such as Giratina). If that's so, how can there be a shiny version of one of the unique legendaries if there is only one of them per universe.
Since the game operates around the multiverse theory (as explained in OR/AS), could it just be that when you encounter a shiny legendary that you are in a universe where that specific legendary is in it's shiny form? This would also conveniently explain variations in IVs and Natures for unique legendaries.
inb4 it's game mechanics
Just because it's game mechanics doesn't mean it lacks an explanation.
Anyway, what do you guys think?