My guess in going back to pre-HW expac Yugiri -- when she first dropped Au Ra were not available to be played, so there is no coding for her reacting to the WoL being an Au Ra. I doubt they'll ever go back and add that.

As for the Raen in Wolves Pier I have no idea when he appeared, but it can be safe to assume it's after HW dropped and he happened to be another refugee.

Now that we're post-SB, however, the lack of Au Ra is still a little odd. Xaela are still more plentiful, and the only Raen I've seen are the Sui no Sato, the pirates (which you wonder if they're from Sui originally), the NIN NPC, a WVR NPC, and the girl from the Ivalice questline. I don't recall any 'wild' Raen in Kugane or even in the rebel forces/Namai, and there's even a random Xaela in Kugane at Pier 1.