Actually, I just came up with an idea that would radically change the appearance of the ship, but would solve the arm problems. Make a cage that covers the underside, with a bay door in the hull, maybe with some kind of rock grinder included somewhere.
The engines would then have to be moved to the rear of the ship, a-la Shire, which would help to reinforce some line continuity. Solely using tractor beams would be a massive waste of energy too. Tractor beams could be used to drag rocks into the cage where they could be demolished, then drawn inside the ship for processing though.