Peter,
Have I gone off the rails here or is it something to do with airframe, ie inlet, and engine accounting?
It's just the accounting. Normally to calculate thrust one takes the momentum change from freestream conditions (ahead of the intake) to the exit conditions just behind the jet pipe nozzle or fan. Between those two 'stations' the momentum is fluctuating as the flow goes through intake diffuser/compressor stages/ combustion chambers etc. Momentum drag is calculated from that initial state ahead of the powerplant.