Enhancing open world / immersion / lore

[Skies]

I cleared Stone Vigil for Ishgard and it just fills back up with dragons and it remains a dragon stronghold?

Just a note on this case in particular.
You did not clear Stone Vigil, the Stone Vigil is a lot larger than that (if you look at the Stone Vigil map and compare it to the Steel Vigil that is up in open world you will realize that you were only in one of the wings of it). All that you dead was sneak in and recapture a forgotten airship, the Stone Vigil is still dragon territorry.