I agree that it's not relevant who the wasted money goes to to the systemic effects, but it certainly implies a very different motive to say the government is taking that fee.
Competition for the limited supply of licenses would manifest itself in other ways, resulting in $200,000 worth of economic resources being used, on average, to acquire a license.
More importantly, the high market price of a transferrable license indicates there is a shortage of taxis relative to demand for taxi service, which has a cost for the economy.