I think I'm beginning to see the light here a bit, FS. What I find particularly interesting is the implication in your post (if I've picked it up correctly) that the fuselage and wing cross-sections may need to be considered separately. To take it to its logical extreme, would it be valid, for example, to consider the cross-section of a pair of wing tip-tanks in assessing the "area-ruledness" of a design? In other words, would the presence of those tip-tanks (assuming they were designed as permanent fixtures) need to affect the shape of things at the fuselage/wing root? Is there, perhaps, a threshold separation distance beyond which components of the total cross-section should be considered as separate entities rather than as parts of the same overall entity?
Hoping, as usual, that I'm making myself clear in spite of my lack of exposure to the relevant disciplines.