You'll need to examine the change location events in the Story Manager system.
WIChangeLocationNode -> WIChangeLocationNodeA -> WIChangeLocation09.
You'll probably be able to tweak some stuff in your location keywords to prevent it from happening. Worse case, you can disable the WIComplexEventsEnabled global variable. It's set to 1 usually but if you set it to 0 then the dragons won't spawn. Though I don't know what other side effects that might have. Should be enough info in the event conditions for you to act on.
You'll also need to be aware of one under "Script Event" for quest WE04.
WEQuestNode -> WEDragonQuests -> WE04 "Dragon vs Player"
You'd NOT want to remove the LocTypeHabitation and LocTypeDwelling keywords because then the radiant system can't use those locations for anything that those keywords will pick up on.
Assuming you're willing to risk the incompatibilities, yes, you can add conditions to these event nodes to keep Falskaar from triggering them, but it's better to try and work out how to manipulate the globals that control things instead. So long as you make sure those globals get reset back to what they should be when people leave.