Eh, I just think that that kind of thing is used, you know? Kind of tradition.
Well, having the primary gun controlled by the pilot alters the way the vehicle is used. Mainly, it allows the vehicle to be used by a single person while still having full access to it's weapons.
Take the Twin Blade Heli for example. As it is, the pilot can unload all of his passengers and still be able to use the craft's guns. If instead the gun was controlled by a passenger (which would be more realistic) then it would require two people to man safely. If you wanted to transport within friendly territory however, you shouldn't need the gun.
But in the case of this ship, I think having the guns controlled by gunners is a good idea. A huge ship shouldn't be flown by one guy.