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No, this is really strange! When I saw the Dark Elves on the surface, it actually upset me.
Maybe they can be excused by the fact that a mountain is "implied" above their castle?
As for how to justify the Mages, I know: presumably, their castle is always in the sky, and the entrance portal is underground. The battle doesn't happen by lowering the castle itself to the ground, but by lifting the enemy to this flying island.
By the way, the same logic can be used to justify the Drow dungeons.