I am missing a policy how sys.path should be altered.

We run a custom sub class of list in sys.path. We set it in sitecustomize.py

This instance get replace by a common list in lines like this:

sys.path = glob.glob(os.path.join(WHEEL_DIR, "*.whl")) + sys.path

The above line is from pip, it similar things happen in a lot of packages.

Before trying to solve this with code, I think the python community should agree an a policy for altering sys.path.

What can I do to this done?

We use Python 2.7.

My guess, unfortunately, is give up.  There is too much code in the field that replaces sys.path with a regular list.  What you propose is effectively an impossible social engineering problem.  You may well also run into issues where the Python C code calls list methods directly even if sys.path is a subclass of list. (I don't know that that is true, but there are certainly places where the C code does that kind of thing).

Could you get consensus to change stdlib and pip practice?  That's at least conceivable.  I guess python-ideas would be the place to start for that.  I'm going to close the issue, since this would be a PEP level change if you are successful.  (Frankly, I don't think you are likely to be successful, but I don't hang out on python-ideas so I might be wrong :)