It's just aeronautics convention. It doesn't matter what value you use as long as it's consistent if you're analyzing a given airplane (e.g. comparing same fullscale aircraft with modifications, comparing fullscale vs. the same windtunnel scale model). Traditionally S is calculated from the centerline of the fuselage outward but it doesn't have to be.
Tango
412th FS Braunco Mustangs
