The sys module gets initialised in _PySys_UpdateConfig() in Python/sysmodule.c. It gets called later in pylifecycle.c. But it ought to just copy directly from the config.

However, it's the site.py module that actually updates sys.prefix for the venv. So you may just be inspecting at the wrong point? Or possibly it's in a codepath that doesn't run on macOS because *previously* it was being set correctly in getpath instead of being deferred until later?