Bit out of my knowledge base, but do the airlines pay the military for this stuff? I know they pay Airservices ( and handsomely, given the consistent monopoly profits) for all sorts of things, but I haven't heard of fees paid to the ADF - do you know what they're called or how they are designated?
Good question not sure how the accounting's done but the military don't pay any fees to use YPDN/YWLM/YBTL but the civilians do. A A320/737 type aircraft would yield between $8-9000 per turnaround at Darwin depending on pax load. That's nearly 12 mil a year if there is only a few flights.
I would guess that the RAAF are paid by ASA or the airport to provide a ATC service. They would be considered a sub contractor as such. If they're not I would love to know where all the money goes for enroute and landing charges then.
With adequate resources, any problem has a solution. The point you seem to miss is that airlines and the tax payers would have to pay a lot more coin if it weren't for the ability to joint-use military facilities. (through either base relocations to even less desirable places, or completely new civil airports)
Well the tax payers would be paying much more. I don't think it would cost much more to run a civy airport as there is much more traffic to fund it. Joint users are a cost saving measure for everyone and they work fine as long as the safety standards are maintained.