Wycombe: I think MSE need to play-up the opportunities that routes like this give for hubbing through AMS to long-haul, so avoiding the UK's now outrageous long-haul APD rates.
If the journey is on a single ticket/single fare, then APD will apply as normal. Buying two tickets at seperate fares will avoid longhaul APD but will be more expensive and will not guarantee connections.
... unless they use a 19-seater, in which case no APD will be payable on the entire journey.