Well, Raen and Xaela both showed up in game at the same time, when the expansion hit. If you take that as canon (because hey, why not?) and assume that both bloodlines arrived in Eorzea ICly at the same time, then the how is clear: They arrived with the Doman refugees, same as the Raen. The Doman rebelled and were able to get away, but they probably didn't rebel in order to take ship out of there. They probably rebelled to hold their land. Leaving was their last-ditch retreat. I could imagine them possibly holding out for a year or more while the Garleans got together the force that would finally crush them. This would give time for word to get out about this hold-out nation. Time for Xaela refugees to flee to Doma. And then, when the Garleans finally did conquer Doma, some of these Xaela would be able to get out on the same ships that took the Doman and Raen refugees.
