I wonder whether the cheapest way to procure VIP government transport isnt indeed by a charter from the private sector. By committing to a minimum number of hours per year you can secure a reasonable cost, and even get to call the shots on livery if you commit to enough hours. Im guessing that the market is pretty competitive at the moment. Rather like obtaining your car on PCP instead of purchasing it. Avoids the oncost of it being operated within the RAF, maintaining separate airfields, and all the squadron number / Royal flight mumbo jumbo. For those concerned about such important (?) people being flown by "civvies" isnt that the default option anyway?
All seems, for once, remarkably sensible to me.