The treasury statement says that the discount is for "direct long-haul", so I would guess routings via other UK airports will not attract discounted APD -interesting what other airlines will say about that, would seem to give CO a big advantage.
I'm not sure what happens for CO connecting pax though? Does a pax travelling for example BFS-EWR-ORD get the APD discount, after all, that's not a direct flight to BOS.