The 747 top deck mod smoothed out some area ruling issues which is one of the reasons it could go faster.
Lift is always carried on the body. A fuselage in longitudinal cross-section has camber so it will create lift at zero angle of incidence. If you think of a spanwise loading distribution graph, the best one as we all know is elliptical for minimum induced drag. If there is no lift on the body it can't be elliptical. It is optimised for the primary cruise design point with (amongst other things) wing-body rigging angle and wing twist distribution.