Ah, yes. Makepanda currently expects the copy of Python to be in the thirdparty dir since it wants to bundle it along into the installer.
I suggest that you either copy (or perhaps symlink) the entire Python installation directory to the thirdparty dir. Otherwise, you could try editing makepandacore.py, looking for SdkLocatePython, and set SDK[“PYTHON”], SDK[“PYTHONVERSION”] and SDK[“PYTHONEXEC”] yourself.