There are issues in the configuration of airports in game, even if PAPI and ILS do not always match in real life and charts indicate that discrepancy too.
One of the most relevant recent cases I can remember is St. Gallen (LSZR), which is and official handcrafted airport. The latest charts I found for LSZR are dated on Jun 2022 and PAPI data are included in the airport information chart:
As you see charts clearly indicate that PAPI has 4º for runway 10 and 28. ILS10 is not standard in this airport and has a 4º glide slope too. However it´s also true that the ILS10 approach chart also indicates that you should not undershoot PAPI below decision altitude due to obstacles (in particular there´s a warehouse very close to runway axis). To make things even worse PAPI is too close to runway threshold in this case (as in real life).
Anyway, following PAPI indications in game produces this result: you are at 30 ft when you did not even reach the runway threshold.
In game PAPI has an apparent elevation of around 2º when you follow 2 whites + 2 reds for this runway. And if you try to follow it that results in no proper obstacle clearing at all and places you always much below the ILS glide slope indicated by localizer. This 2º value is the half of both the ILS glide slope defined in the charts and also the half of the official PAPI elevation declared in the charts. There´s an offset between both systems as PAPI is too close to threshold, but PAPI is still providing the half of the elevatation angle it should provide.
To calculate the appox PAPI elevation in game you can just use the radar altitude at a known point (the fences in the picture) and the distance from that point to the location where PAPI lights are placed (you can measure that in a satellite image using Google). This is just an estimation anyway…
Something appears to be wrong in PAPI assets elevation setting in game as this affects many airports as other users have reported. If you set PAPI in game editor using the elevation defined in the airport charts you will never get a proper obstacle clearing on final. This is what I saw after testing the system with SDK when I placed PAPI lights in my addons at least. Either the elevation formula is wrong or the lights sequence changes are wrong, but there´s something there a bit not consistent I would say.
Cheers