>>40539145Diamond and Pearl give the explanation that Cyrus uses the Red Chain to catch Dialga/Palkia because if he used something like a Master Ball for example, he'd only be able to use a weakened version of their powers and thus not be able to create his ideal universe. It's most likely something similar with Arceus.
It's also possible that, being god, he's doing what some deities in the various religions/mythos do by sending down an Avatar with a fraction of his powers to test your worthiness. Because he's god, of course he's able to make the Avatar be caught by a Pokeball.
