Updating the source package is easier for one. Ubuntu's packages are often out of date, especially if you are running an LTS. It also integrates nicely with virtualenv which makes managing dependencies easier, via pip freeze.

System package's availability vary a lot with the distribution you're using. For instance I use Debian and my web hosting provider is based on CentOS and share my REQUIREMENTS.txt file.I can't really depend on the packages being available on every distro's repository, let alone the same version.

Also, I wouldn't like to install some packages system-wide (a friend's personal project from a github repository) so I use pip and virtualenv in a similar manner as the article recommends to maintain a per project dependency library.

That's how I see it :)

System packages install globally, pip can install globally or inside a virtualenv.

System packages are going to miss some package that exists in pypi. Using pip is also good if your company maintains their own internal toolsets, and want to be able to easily reuse those across multiple applications.

virtualenv can't isolate your system's package util like it can isolate pip.

if you have multiple projects on a system you may have different dependency requirements. module with version 1 for one project and the same module with version 2 for the other project.