To keep things simple we use light displacement as presented by spring*.
You´re right in that misc weight is "empty room" and not part of a carriers structure when looking at the ship only. Thus one shouldn´t be forced to pay for it.
However, we still pay for it. The material spend is defined as the material necessary for the vessels air wing, spare parts etc. You know, the planes are a carriers weapons as guns are for a battleship - and you pay for the guns when building the latter. So you should also pay for planes on a carrier.