"My main point isn't that it is normal practice in the services. I am well aware of that"
DoG, perhaps you'd like to share your vast knowledge of Service life and Chinook ops with the rest of us?
HRH was allocated a number of training hours on the Chinook; it is about the most relevant Operational type at the moment as far as he and his army colleagues are concerned, so of course he wanted to fly one. Now, to fly a wokka through the lanes is perfectly normal for training, as are city centre HLSs (At least they did Woolwich barracks not Armoury House!). To complete a trip with low level and a landing at a different airfield is also routine, as is to carry a spare crew "dead-heading" to reposition the aircraft in these days of high Op tempo.
Bottom line - The aircraft is paid for, the hours are paid for, the crew is paid for. Get over it.