Point the first: The hypothetical situation does not apply, as the conditions for it and the conditions of the actual calculation don't even begin to line up.
Point the second: Your lines of "Determining cover" should start from the base of the 'figure', not 'anywhere on the figure', otherwise I could draw lines of Cover Check from a dragon's head to loom over cover that lunchmeats... I mean... adventurers should rightfully have.
Point the third: How much of the boat exists under the water?
Point the fourth: Rather then argue the point to ad nauseum as to how far what is from what, let's take it to point that the situation may not have been detailed sufficiently (Flat boats, height to boss), and continue with what we're doing. Ultimately, either this is an unwinnable fight and we're being allowed to roll dice for the DM's amusement, OR us losing isn't a plot point, and we'll pull through. Except for all the folks who are about to die.