Both methods (air time and engine-running time) have valid and reasonable reasons for being used.
From the flight-schools perspective, they are paying for fuel and (possibly) a captive on-board instructor while the engine is running.
From the owners perspective they pay for maintanence when the aircraft actually flies and the engine is producing significant power.
If the ground time is significant compared to the airtime (eg doing circuits at a place where the parking area is a long way away from the runway) then VDO time is fairer because someone has to pay for the fuel (and instructor if applicable)
But if the ground time is small in comparison to the airtime (eg a 4 hour cross-country) then either method will produce a similar total cost and there's not much $ to be saved by speeding-up runnups. After all, the enroute winds on a long trip will have more influence on the total trip time.