I was going to say the same when I read that, it's quite the false assumption that the navigator was always the copilot of a firespray up until you use him in your battle as a navigator, like there is no such thing as a hotshot pilot of a transport or corvette.
That reasoning is as bad as saying you should be able to take a Firespray pilot with a zero pilot skill if he was originally a transport or corvette pilot.
There are many holes in assuming a crew member is dedicated to any particular ship, or that someone who specialized in a particular craft would be extremely handicapped being placed on another craft.Good reflexes and spatial awareness are useful in any craft. Nav coordinates are nav coordinates, regardless of what the hyperdrive is attached to, so to speak.
The biggest reason I can imagine for the no navigator rule is that at 3 points it is so dangerously close to an auto include as one can get. I myself end up only using it at most 2 times in the course of a whole game, mainly due to being pretty adept at judging flightpaths. But even then if it is an available upgrade I cannot think of a single time I wouldn't take it. It is that useful. I feel that Fantasy Flight erred on the side of caution in this instance to not have something that is seen on EVERY huge ship and therefore keep things a little more diverse. This is not to say that it was the right or wrong choice, but the best logic I can see behind it.
At the end of the day the presence or absence of navigator on huge ships is not going to make or break them.
