It was revealed in HGSS that Mr. Pokémon had obtained the Red and Blue Orbs from his friend in Hoenn. The orbs had been guarded at Mt. Pyre for thousands of years before the Magma/Aqua story, so it would make no sense if it turned out that the Mt. Pyre couple parted with the orbs at a time when they feared the outcome of awakening Groudon and Kyogre. They had to have given the orbs to Mr. Pokémon (or possibly to May/Brendan who then gave them to Mr. Pokémon, whom they would know from their past in Johto) after Groudon and Kyogre were no longer a threat.
Bear in mind that the above explanation does not assume that the Embedded Tower's Weather trio are necessarily the same ones from the Hoenn games (although I'd say that's very likely to be the case); all that matters is that we know for a fact that the orbs originated from Hoenn.



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