You can apply Admiral cost across the entire fleet because the Admiral is the only card in the game that affects the entire fleet. The RRG and FAQ refer to assigned Admiral cost under the guise of calculating poitns for the ship he was on when you destroyed it. Up until the point in which his is destroyed, because of the way in which he functions, his cost can be applied to the entire fleet.
But the only cost we're (or at least I'm) interested in is the opportunity cost: how many points will I gain by killing that ship. For me sending 50-60 point ship to get 50 points AND guarantee its survival is a good trade even if this ship won't accomplish anything else in this game.
Well, that's assuming that you only use specifically 1 commander. If you use Dodonna, the entire reward for killing the flotilla is 38...still far cheaper than the majority of investments required to kill that 18 point ship within the span of a battle. It's also assumes your opponent doesn't intercept the squadrons you send or broadside your dispatched ship to death.
