TM, the term "area ruling" normally applies only to the slipstream airflow along the longitudinal axis of the fuselage and wings. The wings (root to tip) are in fact taken into consideration when calculating the slipstream cross section.
Maybe I should've left out the comment about the wing and its cross section when discussing "area ruling". The wing has an axis perpendicular to the fuselage axis, and it has its own cross section called the airfoil profile. This is really a completely different area of optimizing shape for delaying the onset of transonic drag. Super critical wings have airfoil profiles (i.e cross sections) that manage the acceleration of airflow over the surfaces of the wing, to delay the creation of local supersonic airflow, and the subsequent creation of shock drag. The design work on the wing cross section exists in at least 2 parts, namely to create a shape that both generates lift, while still managing the speed of the local airflow.
In the case of "area ruling" the slipstream airflow down the fuselage, the idea is to manage the airflow to delay the creation of local supersonic airflow, usually without the emphasis on creating lift at the same time (whether lift is actually considered would depend on the airframe's intended purpose).
The 2 design processes (area ruling and super critical wings) have in common the desire to delay local supersonic airflow, but have a lot of different goals otherwise.
I think I might have confused things by mentioning the wing cross section in the previous post. But I decided to mention it because the wing cross section does contribute to the overall frontal area (and thus the longitudinal cross section) when doing "area ruling" design work. Again, go back to the illustration in my previous post to see how the wing contributes.