While I'll be first in line to criticize the overall Python packaging-story, you also have to consider how Python itself is being used to implement the underlying platform which the OS's package-manager depends on.
If you allow the pip to make changes to things already present on your system, it make break expectations other parts of your OS may have.
And especially given Python's messy package-management story, combined with the less-than-ideal Python2 to 3 compatibility-story, transitioning a full OS and platform from Python 2 to Python 3 without breaking stuff is no small task.
I'm amazed it even works, and that's before you allow users to mess around with packages using pip.
If you allow the pip to make changes to things already present on your system, it make break expectations other parts of your OS may have.
And especially given Python's messy package-management story, combined with the less-than-ideal Python2 to 3 compatibility-story, transitioning a full OS and platform from Python 2 to Python 3 without breaking stuff is no small task.
I'm amazed it even works, and that's before you allow users to mess around with packages using pip.