In my opinion, GF knows the Elite 4 Glitch and knows that it allows to catch Darkrai and Shaymin in D/P (but not Arceus). It is possible that they know the Tweaking Trick as well, but it couldn't be used to catch Arceus back then.
Thus, while conceiving the bank, they blocked every Shaymin and Darkrai caught on D/P. It is possible that the bank allows the distributed ones (Darkrai ALMIA and Shaymin TRU) to pass. I don't know anyone that has them to test it.
However, they didn't secured D/P's Arceus, since there was no way to get one.