Looking at sitepkgs.py, the current implementation only looks for PEP 561 packages in site.usersitepackages() and site.getsitepackages(). My environment has a sitecustomize.py that adds additional paths to sys.path based on some in-house env vars (not really my choice, I inherited this setup). Could we add a mypy flag to indicate that it should use the full sys.path? I don't really see a harm in including PYTHONPATH too.

On a related note, shouldnt user site packages have precedence over system site packages?