That XKCD is more about messing up your system by not knowing what you're doing but randomly following shitty tutorials which suggest stuff that collide with each other... Python's only fault in this is that it's a simple language and thus attracts people who aren't software engineers (students and math majors) and thus mostly don't know or care how to keep your system clean but love writing tutorials.

It's pretty easy to keep your pythons clean, don't use conda, never run pip with sudo, never run pip with --user..., never run pip outside a virtualenv (a good safety measure for that is to have pip point to nothing in your user shell, you can access system python with python3/pip3 if needed)... To check your python is clean, create a new environment and run pip freeze, it should output nothing.

pyenv is a non-destructive system for managing multiple pythons and virtualenvs (all pythons and envs get installed into ~/.pyenv), pip is a good system for distributing dependencies (when library authors don't skip out on providing binary wheels, and software authors use pip freeze to generate requirements.txt files).