Beagle, the dayglow strips on XH478 are at the top of the fin, on the nose behind the radome, on the ECM housing and (possibly) on the wing tips. I guess they would fit-in neatly with the aircraft's refuelling trials but the dates don't tally, so it's hard to work-out what they were applied for.
On 539 the black rectangles are in a line, straddling each side of the bomb bay doors along the centreline. I've seen these markings (rather foolishly) referred-to as camera ports in the past but they're obviously calibration markings associated with weapon drops of some sort - the clue's also in the camera fairings attached under the wing tips.
Exrigger, thanks for the pointers