RAT 5, Re “what … should be flown as target if there is a difference between PAPI & ILS G/S?”
You seek an ideal solution from a complex situation. If the ILS and PAPI ground installations are well harmonised and the aircraft GS/eye height is small, then the height at which there is any significant difference might be so low as not to be of interest (see ft’s post). However, very few things in aviation are ideal or definable with accuracy; with any difference between the systems it is unlikely that you will know if this is due to the ground installation or the aircraft, a normal or abnormal occurrence.
If the ground installation is non-standard this should be notified on the airport chart, but even this is not foolproof – see the recent accident at Quito where the visual and GS flight paths differed for good reason, but were not identified to the crews; these are unusual circumstances.
Generally use the aid as dictated by your approach – GS for inst, PAPI for visual. In the situation described (visual) use a bit of both. The GS should be kept within half a dot – this avoids any error from visual distortion of PAPI at longer ranges / hot hazy days (light bends more than the GS); use all of your resources – altitude/range, runway position in the windshield.
At lower altitudes / close in, the approach flight path should be assured by 100ft (stabilised approach checks at 500/300ft) thus ensuring an accurate threshold crossing altitude. In poor weather, then PAPI has other values; irrespective of alignment, any quickly changing lights can alert the crew of any sudden change in vertical speed – windshear (vertical or horizontal).
Much of the above comes with experience; thus it is important to observe and note the many parameters which go into the judgement of the flightpath during an approach. Whether you are monitoring the PF or the autos – neither will be perfect, but they should be good enough – within specified limits (SOPs). Build up a mental library of approach paths and the items which define them, then when the GS and PAPI are both u/s you have something to use as approach ‘guidance’ even if this situation has not been practiced previously.