Thinking about it, I just realized that we really have no idea where the playable Au Ra are coming from. They didn't all come with Yugiri from Doma, or we would have seen more hooded people running around. This is a crazy idea, but what if the Au Ra are already IN Ishgard? Like, the clergy have known about them since back when Shiva was around, and they have secretly been a part of Ishgard society and culture for a while. While that's a real longshot, the fact that Ishgard is closed off from the rest of the world might hide their presence, and it would explain why they are suddenly abundant in heavensward.

It's kind of like in a movie when you find out the leaders of the government are all vampires, or that the government has been silently tolerating aliens living among us. The racist Ishgardians have been doing foul things due to evil influence, the dragons begin a new war in retaliation, and only the hidden half-breeds in the city are able to rise up and stop the fighting.