It's been a while since I played Riven, but I don't see any inconsistencies here. As I understand it, none of the paths are below sea level. The water that you pass through in the golden elevator is not part of the sea, it's a small indoor "pond" that's suspended by heat, and the elevator goes through it for aesthetic purposes. And the large window where you can call the wahrks looks out into a fish tank as far as I know, on top of which is the linking dome and the Riven map. Those are quite far above sea level, and if you ask me, there's enough room to fit the large wahrk window under there.