Joe-
If you consider the total cost or buying two policies, vs. what could go wrong, a lower unit, a T&T, a computer, blow a block or camshaft seal, and the worse case a powerhead, you are essentially prepaying for all of these and the better part of a power head. The chances of one engine having trouble - it could happen, but both engines, that's a very very far long shot.
So why prepay for the work? if something does happen, pay when it does. A single engine policy does make sense, but tripples are even more so a less attractive economic analysis than twins.
The other consideration, only applies if you intend to sell during warranty period, is the valve you gain as a seller. As a buyer I would find the boat more attarcative over others, and pay more for it if it had remaining Yamaha engine warranty.