Well, it bothered me...if only because I used to package software, etc. for TurboLinux US and have helped with lots of Debian packages. I kept looking at it but I never could figure out how to make it better.
Perl is now, mostly, under control for me because Bugzilla (for example) installs the CPAN libraries into it's installation...which is great. Ruby is starting to be better for a similar reason: Bundler.
BTW: The article forgot to mention that unlike other interpreted languages (perl, python) you can install multiple versions of the gems and request specific ones when you 'require' them. Which means that having the Distribution manage the gems is a lot less important -- You can lock them in from the application (manually, or with something like bundler).