First, this is important to me. I don't see a 'boat mode' listed in the notes via the link you sent, did I miss something? Please point me to the text that talks about 'boat mode'.
Second, I think they can handle it with a 'dynamic home point' (aka: Return to me) where the controller will periodically (perhaps every 5 or 10 seconds) send a new home point to the copter as the new RTL point. Also a mechanism should be there to have the option to have the copter hover and wait for a land command (unless power is about to deplete).
I wish I could get someone to think along these lines, I think it would be perfect, I'd be glad to test it for them (I have the boat)!
Another problem is that the sensors need to be able to calibrate when the boat is rocking. So far I have found this is a larger problem than the others.