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I have Two theories.
It is implied in the delta episode that in the non mega timeline they got rid of the meteor by sending it into another dimension
The mystery dungeon games involve a plot talking about an out of nowhere meteor containing deoxys who threaten the world and must be destroyed by rayquaza.
it's the same meteor.
in the movie hoopa and the clash of age they use an amulet who seal the pokemon (pic related )
it's the same motif around arceus because the form of arceus that we see is a limited projection in 3D space so that we can understand it.
