I'm always confused by these sorts of posts because they happen often so there is clearly a problem but for some reason I've never had much of an issue. I've been using and developing with Python for about 15 years. In that time I've worked on Python projects large (OpenStack) and small (gabbi) and taken over maintenance for some old standbys (wsgi-intercept, paste to name two). Dealt with the 2->3 transition. Released a whole bunch of things to PyPI and relied on far more things that I've pip installed from there. It's been fine.
I don't know what I'm doing differently.