I have gone over my model as well. Everything functions in FSX/Accel. More specifically, nav and beacon lights show up, VC and exterior cockpit transparency is clear. This is an FS9 portover reworked to try to get it ready for the RTW Race 3 years ago. I can't remember for certain, but it's possible that P3D at that juncture was able to accommodate these older models or P3D was not a concern at that time and it was never tested in that Sim. If anyone else has more direct knowledge I wish they would speak up and assist here. I have the latest version of P3D and as you've obviously discovered, while the switches function, the VC does not respond to the alpha for the glass and the nav and beacon lights don't function.
Without any other input from someone who has this particular "revised" version working in the latest version of P3D. . .it is my assumption for the time being that as an FS9 portover it is not compatible.