> 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.