I do want to warn you (again) that the system is designed to work for Python programs, not C++ programs. You will probably have less trouble if you generated an installer for your C++ program the other way.
These are the difficulties faced with running a C++ program in the runtime environment:
(1) .exe files or .dll files cannot be run from a. p3d file. If you want to run them from a .p3d file, you must extract them. Using the -x option will help if you use pdeploy since extensions marked -x will be extracted to disk by pdeploy.
(2) The runtime distribution of Panda3D uses a different set of DLLs that I’m not 100% sure are compatible with the ones in the SDK, since they are compiled in release mode with NDEBUG set.
(3) Panda needs a Python entry point, as you have already discovered.
You can run an .exe program with one of the Python os.exec* functions. The code I gave you should provide the path to the .exe file, but I’m not 100% sure. I suggest printing it out to check if it’s the right location.
Again, I want to emphasise that using a third-party tool to generate the installation wizard is probably going to be less effort than trying to get packp3d to work for C++ programs.