Not sure if it's typical or not but it sure sounds like the way this one designer does it.

I believe that you'll find that what Paul said about the rule book including the fuselage area is the case.

As for the plans and the designer it's possible that when he did his wing area calculation he did not use CAD and instead estimated the area of the odd shaped areas like the tips and did not include the fuselage for some reason. Your AutoCAD measurement is likely far more accurate.