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My guess would be that there's a Psychic Pokemon behind the "fourth wall". LOL Levitating the Pokeballs, making them glow, and even shrinking the Pokemon to fit inside them. As for the Dark Pokemon shown going in and out of Pokeballs, maybe it's an all-powerful Psychic Pokemon... Like Mew-Three!!! LOL
I say that Cthulhu who dreams in Ryleh is the one dishing out them balls. Shrinking and glowing, returning and flowin. The stream of insanity is only unknown. - Kobold Asylum, "Parallel"