Is the cost - time, money, stress - of flying to an EU airport on a separate ticket worth the alleged higher costs of a flight from GB?

If you have an itinerary that allows you to fly from outside the UK AND it saves money (which it might not) then consider it, but don't just look at the APD, say "I don't want to pay it" then subject yourself to extra travel time / travel costs / worry about missing your next flight to "save" money.