I think OP does have a valid Point on the matter at hand.

Ground based Mounts, such as for example, the ARR Beast Tribe Mounts which totally shouldnt be able to fly in the first place (except the Kobold one) should have instead, increased Movement speed in comparison to Flying Mounts. It isn't a big thing to adress, but i think it would be in a Asthetic way, way better looking.

Also, on the matter with the "lol its aether, i dont have to explain **** why a Elephant can fly" excuse, if you really want to cover lore on this, kerp in mind that the overall density of Aether is fading as stated at the beginning of Endwanker, that alone could be made as a valid enough reason why certain Mounts cant fly anymore.