The specific fortress you're referring to is Stone's Flying Fortress. I don't know that the specific fortresses are referenced for their purpose, but there are a few quests that your platform operators send you to retrieve items from them. Also there are many powerful armor set pieces from the bosses of the flying fortresses.
If you're looking for story as to why they're there, well they're Damian's lieutenants and commanders. They're staging an attack on Rivellon. You want to stop said attack. That's about as deep as the plot goes =p
As you've discovered already, it is worth your time as there are a loooot of things to fight there.
Concerning the anti-dragon zone, you'll eventually discover teleporters that you can use in human form.
Last edited by Dandai; 16/11/10 09:06 AM.
