Personal head canon is that your not actually capturing the god pokemon, just corporeal avatars they use to interact with the mortal realm. Its the only way something like this makes sense to me.
The only game where you actually fight Arceus is in Pokémon ranger, though you have 3 members of the creation trio with you (the only pokemon even able to challenge Arceus let alone beat it), but you only succeed on calming it down till it stops fighting.
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