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As I recall, you can jump between islets using Dimension Door in the Dungeon, but you cannot fly over them. That is to say, while you can fly over impassable mountains on the surface, own below between the islets it's like a solid wall with a ceiling, as in a cave—you can only fly along the corridor. And flight follows a conditionally straight line, meaning you cannot turn around a corner mid-flight without an intermediate landing—and landing on water (without a boat) is impossible. I believe that's how it works.