[Agrajag]

The way I see it, fly gives you the ability to ignore terrain handycaps and enemy territory handycaps (you can't go through one enemy province to another if there is another one in the middle).
So what it means is that you move through all three provinces (if you have strat move 3), theoretically parking in each province for a few days during the turn (which is a month long).
So if your units can't go through water provinces, they can't park in them so they cannot fly across bodies of water.

That is more a matter of how you percieve the game, but technically (game engin-wise) it is impossible to fly over sea provinces as if you are sailing over them.