The point is the bomb bay wasn't designed around the improved defensive armament from the E model on. The bomb bay, and its limitations, is something that the B-17 was stuck with throughout its life.
correct. The B-17 had a conventional low-wing configuration that was in some respects outdated by the 1940's. It was thick and heavy which of course made it very strong but the spar attaching the wings to the fuselage constricted the area available for the bomb bay, inhibiting the bomb load. So the defensive armament had nothing to do with the Fortresses's limitations on bomb loads.