Hi Sector 7G.. I'm a retired old codger, but did work Heathrow Tower for many, many years.. I recall the countless times I did pretty well what you heard.. An aircraft on short final for 09R and the next departure taxiing down what I will call "the extension taxiway" (probably got some other weird name now). Using the specific clearance "At the threshold, line up and wait", and emphasising "threshold" I did not add any condition on the basis that the lander was going to be past the threshold by the time the departure reached there.
I have also, probably thousands of times, cleared Checker unconditionally to enter the runway whilst an aircraft was landing, on the grounds that the lander had passed the checking vehicle. If the aircraft was still airborne, approaching a displaced threshold, I guess some pilots might have wondered what was happening but nobody ever queried it. In such cases I guess you have to trust that ATC knows what it's doing... most of the time!
I was just trying to think of reasons why you heard what you heard at that particular stage in the flight.... now back to the rubber ring and Horlicks.