Nothing here overrides there system wide Python version.
The article specificially goes into why not to do it.
> pyenv allows us to set up any version of Python as a global Python interpreter but we are not going to do that. There can be some scripts or other programs that rely on the default interpreter, so we don’t want to mess that up.
Using the Python interpreters in your system doesn't mean you can't make virtualenvs out of them - it's just that they are precompiled and well supported on your specific OS.
I used custom Python interpreters a lot and it's nice to be able to rely on the system to provide a sensible environment instead of forcing myself to build my own.
The article specificially goes into why not to do it.
> pyenv allows us to set up any version of Python as a global Python interpreter but we are not going to do that. There can be some scripts or other programs that rely on the default interpreter, so we don’t want to mess that up.