It's just a piece of 2.0 flavor text that hasn't been updated for 3.0, that's all. Stop trying to read too much into it.

The Au Ra are still a rare species in Eorzea (there's like, what, 4 named Au Ra in the entire game?), but are considered one of the Spoken races. That said, they did / do face prejudice (go talk to Sidurgu, and I hear the WHM antagonist was a persecuted Xaela as well).

The rest, well, who knows. Presumably the Five Spoken races of Eorzea have accepted each other since the beginning of the Sixth Astral Era, but without records we have no way to prove anything.