In order to include the mass of components on the inside of an aircraft, you need to use the priority flag. When parts of a volume overlap, the highest priority density is used -- otherwise, the first encountered is used.
You can use both volumetric density and the thin shell density. If you want to model a thin shell filled with air, set the volumetric density to zero.
Unfortunately, the thin shell density is only included for components that contribute to the OML of the aircraft. So, if you have a hollow object inside the airplane, the thin shell contribution will be dropped.
You could use a separate set and perform the calculation twice if you _really_ needed to handle that case, but you can accomplish a lot the way it is.
CompGeom will calculate the volume of components. If they do not contribute to the OML, their volume will be discarded in the 'wetted volume' calculation, but the 'theoretical volume' calculation is what you are interested in.
Rob