The new footage of Bismarck in the 3.0 benchmark shows him leaping and diving through the clouds like a whale or dolphin would the sea. It's entirely possible that he was originally an aquatic creature and gained his flying abilities as a result of his summoning.

We still don't know much about the origins of the new beast tribes. We know the Ixal and Moogles believe they came from a floating continent in the skies (possibly THE floating continent we're confirmed to be visiting in Heavensward) so it may be that some of the new races up there actually came from the ground at some point. There are plenty of ways to explain a cultural crossover of some kind between the races. I'm sure this will be explained in Vanu lore.