Well in ten years I have never had a nuked server by pip or virtualenv. I am sure there are edge cases but that must be true for all the ways of deploying stuff. I guess the ones you know well appear simple to you !
I kind of agree with both of you. I don't think Python deployment is that bad, as most modern managers get it right (I prefer Poetry nowadays). However something like letsencrypt-auto, which AFAIK installs its own dependencies, is not something I'd run. I've actually never used it precisely because it's too magical. Programs shouldn't install their own dependencies anywhere outside of a virtualenv.
Does certbot do the same ? I don’t use either so I can’t tell.
I strongly agree that any python program must install its dependencies in a virtualenv. One could even argue that this principle could be extended to any software !