Example 1: Using System Python on Debian is a notoriously terrible experience for example, because they split up the venv module from Python itself and distribute it separately. I've had so many issues because of that and there's no good reason to do it. It's part of the stdlib, it doesn't need a separate package.
Example 2: Debian Jessie shipped with the ancient pip 1.5.6 (https://packages.debian.org/jessie/python-pip - upstream is at 9.0.1 since 2016) which never got updated, just stayed stuck there, wtf? Such old versions of pip are lacking support for a bunch of things that python packages today use on setup, so it would install things in a weird way and then packages would be broken, users wouldn't understand why. One of the many cases of not giving users access to a more recent version of a package, causing the user's experience to be severely impacted (and of course, they won't know to blame debian or the pip version in this case).
Edit: Incidentally, that last bit is why I always, always do `pip install --upgrade pip wheel setuptools` whenever I create a new virtual environment to make sure I don't get issues installing packages.