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Actually, Palkia in Pokémon Pearl was stated to be distorting dimensions by Cyrus. (In case you're wondering where it's said, it's on Palkia's page with a link to it. It's at 11:11)It's just a universe. Why would Cyrus want to destroy anything beyond the universe he inhabits.
It's a single universe. The CT highest feats I've seen outside of the lore of creating all worlds is reversing two timelines, which happens in the anime