It's true that the distro's packages can often be out of date: particularly with "Enterprise" releases like RHEL/CentOS. That doesn't mean that one shouldn't use the package manager, though. Building custom packages to backport updates and tracking the upstream for security and bug fixes isn't the funnest thing in the world, but it is often a necessary evil. It's certainly better than a "compile from source then dump everything into a tarball" approach which leaves you with no good way to track what versions of which software are installed on which nodes.
It isn't a necessary evil when it isn't necessary. If you have isolation (like virtualenv) then each app gets exactly what it needs. Life is too short to waste it trying to make every single bit of Python use the same versions of dependencies, pinning the version in the package manager, etc.
The universe does not revolve around lazy sysadmins
I think that a 'best practice' is to do something like create a virtualenv for your app and package the entire virtualenv in the distro's package manager, then version that.
