Well, according to the tooltip, marids can fly thanks to a "magicked carpets affixed to its back". And those carpets are made by the Ananta, so we probably wouldn't find any wild flying elephants out there.
Still, your point hold for the tyrannosaur as we don't see any wild one in Eureka.
Interesting, so that's kind of a "grey zone" in the lore, right now?
Still, aren't Sastasha's pirates another story? I thought they were modified by the direct intervention of the primal Leviathan. And on this, it wouldn't be the first time a primal modified someone or something. If memory serves, Odin is doing the same thing with the player that kills him. But mutation by exposition to a large source of aether? That's kind of a first, I think.
And for the islands, you are probably talking about the Churning Mists and the Sea of Clouds. And it's true that they have large amount of crystals that generate a lot of wind aether, preventing them from falling. If I remember well, Bismark was actually feeding on those islands. But the tyrannosaur do not have those kind of crystals in it, so the mystery as to why it can fly still hold for me.
And as Penthea said, we don't see any wild T-rex flying around in Eureka.
I need to see the quest text again, but didn't Krile said that those monsters weren't here before the incident of Val happens? (Plus, how can living things survive a dimensional compression...?