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It looks to me that when a Snag Ball is thrown, it opens and sends a "tractor beam" at the target Pokémon while in flight, as opposed to requireing the ball to come into physical contact with the Pokémon. Because the ball doesn't get close enough to the opposing trainer to block it (as they do in the Gameboy titles), the Pokémon is scooped up, and then attempts to struggle out, just like Wild Pokémon.
Remember that "hand" looking animation that occurs when you throw a Snag Ball in Colosseum/XD? And how it doesn't occur in XD when fighting a Wild Pokémon?
Perhaps the Snag Machine hijacks the Recalling function of the Pokéball into being able to "recall" any Pokémon into it.