My apologies for reordering your comments, but I wanted to address them as coupled as my response is interlinked.
I agree that so long as flight exists, seeming to suddenly un-learn how to fly is... well, bull, unless there's an obvious difference in the environment as would affect flight.
For that reason, when I first heard that HW was to have flight I --in naive, pipedream fashion-- hoped that we'd have literal (air/aether) currents that'd supplement a stamina-based flight system. You might, for instance, take a sprinting start before diving off a cliff into a deep ravine, catching a current that passes down and through the chasm, refilling stamina even as you glide or hover (chocobos' obviously aether-assisted flapping). In such a way, topography would still be relevant and, since you'd have to figure out where these (air/aether) currents flowed and how they shifted over the course of the day or different weather patterns, there'd still be an element of progression: there'd be the real, player knowledge component and then perhaps a further, subtle artificial "attunement" bonus by which stamina costs could be decreased and max speed increased with time spent in the zone or along its currents, etc. It'd neither require suspension of disbelief as our mounts repeatedly forgets how to fly just because this zone is arid and has no river instead being arid and split by a river, etc. Instead, flight would only be as different as the zone's topography and a bit of arbitrating randomness (especially if air and aether currents aren't quite one and the same).
But alas.
Same, though locking it behind the extra few sidestory quests seems a little odd to me, even if I understand that it aids the questmakers' ability to slightly push their curation upon the players. I'd still love some actual flight physics and the aforementioned unlock system, though.