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 :)