There's a good reason for this. The average user has no idea and doesn't care what language some random distro-packaged program is written in. They want to be able to run ubxtool or gdal_calc or virt-manager or whatever without setting up a virtual environment. Python developers on the other hand should be adept at such things, should they choose to use a non-distro packaged version of something.

The tricky part is when "users" start using pip to install something because someone told them to.