Well, all that happens is that some IRE mate from the CAA watches from the jump seat whilst you do a bit of routine MCT. Which you have to do anyway for military currency basic training requirements - the difference being that you organise things so that the MCT meets the CAA IR requirements. In my case it was SID, MALBY-BCN and off at NITON, radar vectored ILS at Lyneham, SEFATO then once round the Brize NDB hold and a 3-e NDB at BZN, 3-e go-around and 3-e vis circuit to land. Everything except the airways leg was without autopilot.
And then a cheque for several hundred quid to the nice CAA chap.
Incidentally, these trips also serve to keep the CAA well informed about how the military operates big aircraft - so are of mutual benefit.