Well, it's the only part I haven't tried on Nightmare difficulty yet (except for that situation in the Hall of Echoes-arena where Sassan would one-hit me with Magical Drumfire). But I certainly finished the game in both Flames of Vengeance as a CD expansion and in Developer's Cut, and flying ahead was the way to go.
If there are flying demons which can approach the ship, then you'll have to prioritise those before going after the edifices (and among those, prioritise the spawning towers so that no further flying enemies can follow).
