Why shouldn't a zone transit which I guess is requested to avoid track mileage not have to pay for that short cut?
A zone transit is not a short-cut if it is the flight planned route. Refusing (or not being able to obtain) a transit is extending the normal route.
Control zones are not exclusion zones where you can't plan through and if you manage to get through it is a short-cut. They are fully plannable (within reason) and it should be viewed that a reasonable transit request is not a request for a short-cut.
Therefore it could be reasonable for aerodromes to pay for the resource they use -airspace and receive a reduction in the amount paid based on the number of aircraft that proceed through that airspace. Offspace anyone?