Hmm. Maybe. :) I guess it would register all of the Pokédex data for all of them on my SS (besides, it's not like I'll ever catch my own Shaymin or Arceus without an Action Replay to unlock the items, since I would never randomly plant legendary Pokémon).
The only possible glitch is I don't have a lot of Pokémon to trade out, so this would literally be a couple at a time. And each couple sent back via the alternate (non-official) version would be in turn traded over during the transfers, so you'd have to keep switching games. In other words, you trade from the "wrong" version, I send over a couple for those, then I trade them to the "right" version for two more, which later trade to the "wrong" version for two more...etc.
The only possible glitch is I don't have a lot of Pokémon to trade out, so this would literally be a couple at a time. And each couple sent back via the alternate (non-official) version would be in turn traded over during the transfers, so you'd have to keep switching games. In other words, you trade from the "wrong" version, I send over a couple for those, then I trade them to the "right" version for two more, which later trade to the "wrong" version for two more...etc.