I believe Pokebank checks against hacked Pokemon that are not legitimate. For example, a Keldeo with Giga Drain or something. I think that from the way that a Pokemon is generated and stored in memory there is no way to check the legitimacy of a generated Pokemon other than to validate if the bytes line up with what is legal for said Pokemon. So yes, generated Pokemon are a thing and I don't think Nintendo will ever be able to prevent previous generation Pokegen'ed Pokemon from coming over via Bank. They may have added extra measures for Generation 6 but I'm sure that someone will be able to decipher the algorithm that Gamefreak has employed.
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