The Ninja trainer could be a Doman refugee that arrived earlier before the big blow up in Doma. They were under a Garlean occupation before the refugees rebelled, so it wouldn't be a stretch to say that there was a hidden sect in Eorzea fighting back against the Garleans much like the Ala Mihgans. As to why there would be no mention of them before 2.4, meh they would be very bad ninjas if people had a clue as to what they were doing. Rogue also has a shroud of secrecy that makes saying "They were hidden in the shadows" a viable thing to say.

Then again, if SMN/SCH storylines showed anything, you just need a couple of eager researchers and some "allagan" artifacts to teach a job.