Python Path Problem

Python3 is packaged with two repositories.
!PythonSite and !PythonUser. The former contains python system modules and is installed in Boot:Resources. The latter is intended for user written modules and by default is stored in Boot:Choices:Boot:PreDesk.
When either is booted it adds its location to Run$Path.

However, Python does not use Run$Path directly but constructs its own path to search for modules.
To see the python path, open taskwindow and key;

import sys
print(sys.path)

On my machine, the python path contains the PythonSite location, but not that of PythonUser.

Setting the system variable PYTHONPATH to point to …!PythonUser.scripts will cause !Python to append it to sys.path.

This works but is there a better way and I am missing something obvious?