Yep, just docked in Limsa then got my Aether point and teleported back to Ul'dah. The ferry docks at the same spot where your boat does in the opening Limsa-Lominsa cut scene. You can't just walk on the ferry like you did in XI (*sadface*), you have to talk to an NPC and you'll get a cutscene where you run on to the boat.
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The Adventure League of Eorzea: A progression & RP guild. FFXIV's longest-running RPLS