System package management is a mess in the first place, if you have a program that uses python then all the packages that it uses need to be installed globally, so you have python packages bundled as system packages which can conflict with that same package installed with pip.
> if you have a program that uses python then all the packages that it uses need to be installed globally
Only if that "program that uses Python" is itself provided by a system package for global installation.
> so you have python packages bundled as system packages which can conflict with that same package installed with pip.
Right; you can choose whether to use system packages entirely within the system-package ecosystem (and treat "it's written in Python" as an irrelevant implementation detail); or you can create an isolated environment so as to use Python's native ecosystem, native packaging, and native tools.
I don't know why anyone would expect to mingle the two without problems. Do you do that for other languages? When I tried out Ruby, its "Bundler" and "gem" system was similarly isolated from the system environment.