The exception in the UK APD rules is for conjunction tickets only. Conjunction tickets means that the whole sequence of flights is a single itinerary and a single contract of carriage, even if it is embodied in several tickets (which often happens when you have too many segments to fit in a single ticket). In practice, conjunction tickets are always stapled together, so the separate booklets hypothesis contemplated in the rules remains in effect just that, i.e. hypothetical.
These rules are stricter than the US rules on exemption from US domestic air transportation tax, which only require a reference in the domestic ticket to the international ticket without requiring them to be conjoined. I have succesfully convinced NW to exempt me from US domestic tax on a tickets bought separately but within the appropriate time bounds of an international ticket (it was hard work, though). This would not be possible for APD.