I mean all else equal, the weapon specialist will just be a better shot, because of his characteristic bonus. Also, due to his aptitudes, he's just going to contiue becoming a better shot than the stormtrooper, due to the exp curve.
I mean, on the table top game, the stormtrooper has a much better BS than the guardsman. In fact, the stormtrooper has the shooting capability of a space marine! What the stormtrooper is NOT as good as the space marine in, what the stormtrooper is equal to guardsmen at, is WS! And in Only War, the stormtrooper is suddenly a WS powerhouse, thanks to his aptitude! What's up with that?
I feel like this system is conflicting quite a bit with the empyrical evidence already put in play, already observed by the players, in the table top game.