There is an indirect argument that APD pushes certain transfer passengers towards Amsterdam.
Those people travelling domestically in the UK have a choice to either fly, go by train/car or not travel at all. APD will clearly discourage people from flying when their entire journey is within the UK and subject to an APD charge. The result is fewer passengers on these routes, lower demand and likely lower frequency of flights.
If the number of domestic flights is reduced, it becomes harder for places like Birmingham or Manchester to function as connection-friendly airports as they cannot generate domestic feed for long haul carriers so easily.
Long haul carriers thus see BHX / MAN as losing some of their appeal with the reduction in potential feed, while routes to AMS which exist for onward connections of people who cannot easily substitute train for plane are relatively untouched.
APD has naff all effect on connections via Heathrow but it will affect cities like BHX or MAN