I've seen too many issues caused by relying on the system python. For starters, it's much more difficult to fix if you screw something up.

I tell everyone to use pyenv -- but only to install specific versions of python. I then create a primary venv for a couple of versions, and that's what I use as my "system" version. Each project creates a separate venv based on the pyenv versions. I use autoenv to activate and deactivate as needed.

It's a little more setup, but it avoids so much magic, and it's extremely robust.