We have seen Ganon come back from the dead several times. Mainly without an sword attatched to his forehead, but I'm sure he'll make his way through that, in one or another way. Maybe he leaves his earthly form of Ganondorf (which is the one with the Master Sword on) and ressurects as Ganon...
Ganons placement woudn't probably be the same if Hyrule was unflooded, just as Brandon explains in the text. And I fail to see why the Master Sword would affect the scenario, it's never used (or atleast said to be used) in both LoZ and AoL.
Overall I think it's really solid, actually. I'm...