These things can be compared to and checked for, since you are, after all, uploading your Pokémon onto hte Nintendo Wi-Fi Connection servers. They can moderate any Pokémon that come in and recognise the means of them Pokémon, for instance.
sure, but how extensive can that regulation of team conditions go? you're willing to think that a, let's say, Dratini caught in a faulty area with the "Wild Encounter" code enabled in D/P would be detected by the GTS.
but how far will that go into including possible faulty "Wild Enctounter"-caught pokemon from GBA and transferred over to D/P? i HIGHLY doubt that D/P has a recorded set of data that refers to all of the GBA games' Wild Encounter information.
meaning to say, if i used AR for FR to retain a Dratini in Rt 101 and transferred it to D/P, then GTS would fail to recognize the fallacy of wild pokemon in the GBA game. if they DID have this kind of information inside the D/P cartridges, then there's no reason why they DON'T have cross-generational trading (DS to GBA).
and it is, therefore, safe to assume that if they don't have DS to GBA trading, then they don't have that kind of information implemented into the GTS. if they don't have that information implemented into the GTS, then it's safe to assume that they probably didn't bother countering AR "Wild Encounter" efforts.
this of course, is all from logic and speculation, so i guess we'll just have to wait and see. it won't be much trouble training the available D/P pokemon for the time being anyway.