Why does the RAAF do VIP flying? The answer is twofold. VIP budget comes from Department of Prime Minister & Cabinet. How would it look in the papers if the cost to fly ministers around were to increase by $10,000,000 per year? You think Qantas pilots will fly them for free? At the moment the wage bill comes from the defence budget - hence zero cost to PM department for wages. Second reason: remember all the problems we had sending troops to Timor? Low establishment was the problem. Defence is happy to have RAAF pilots flying the special purpose aircraft as it is a way to increase the pilot establishment. Defence is happy, and it is a convenient way for PM's department to hide some of the costs of what can be politically sensitive, win-win.
As an aside, why would an ex-RAAF VIP pilot who is now in Qantas want to go back to the standby's and waiting around for hours in the jet for the late politician? Have not even begun to think about the industrial implications (but then again AIPA is controlled by the Cadet Mafia that has a chip on its shoulder the size of the Amazon forest about ex-RAAF guys...)