If I understand correctly, the GP model has its reference point at the ARP
How George?
If it is a model then it is placed like a library object. To place a library object you either have to set an explicit altitude AMSL or you set IsAGL. IsAGL with a setting of 0 (the default) will place the object at the Ground Altitude that is determined by its reference point.
There is no altitude information in the Bgl file that is created. Therefore FS can know nothing about that altitude. So I might surmise that the poly will be placed using 'IsAGL' with 0. On this basis the poly would get placed at the altitude found beneath it.
All models to my understanding have a reference point. For models create in GMax etc the reference point is determined by the designer - They are not always in the middle of the objects footprint. So wherever the reference point of a poly or line happens to be when placed the ground level at that point is taken to be the altitude the poly gets placed at.
Now as I understand it the GP Layer matters and each layer number must have some minor vertical (altitude) factor over and above the lowest (which I surmise is at ground level)
I know absolutely nothing about this and these are FS8 objects that are clearly not the same sort of model as FS9 or FSX ones. What I do understand is that only objects that are associated with an airport can inherit the ARP value. Since these include aprons, taxiways and so on I would agree that any poly placed on one of these ought to take the ARP as its vertical placement reference.
Anything off those parts of the airport that are locked to the ARP are not so constrained. Thus they will take on the altitude of whatever the ground is under them. Since we generally place a flatten under the airport so that everything in the airport space is flat (well not in FSX of course) then it is reasonable to assume that the polys will take the ARP reference altitide - but only because the flatten is set to match.
Off the airport background is anyones guess.
So I agree that most of the GP objects that y'all are trying to place should be at ARP altitude but not because of anything inherent in the model or Bgl file.
Finally of course the FSX round earth model may well affect the altitude the GP Objects get.