If a ship, for example a Valor, didn't fire its FG through its FG muzzle, then the whole ship appearance would need to be changed.
However, as such FGs can't fire at an angle, moving the hardpoint to the ship's center and setting it so that when it fires, the projectile passes through the muzzle, is possible. I just don't know how to do it. Maybe Shooter does, but I'm currently too busy to spend effort on testing something that probably won't work.