I did only scan the article, but using having a remote repo hosting service (is it really developing on the server while using git?!) configured, branches for feature-dev/bugs/staging/qa/production, vm configuration via chef/puppet, separated settings files, fault reporting etc etc are most (for me) all a part of doing it the "right way" before writing a single line of my own code.
Heh, at some point soon[1]... once i've migrated the rest of my websites into rackspace cloud & their "next generation" offering stabilises i'll be writing a "This is how we do it now, it might work for you" type article.
somehow i don't think this article was targeted at you. i'm betting if you already know how to run puppet/chef, and have all the above, you already have an opinion on project setup.
True, the bit about developing on the server is straight up odd though (if i skimmed it correctly that is) as I find the debug mode exception screens rather helpful, and I wouldnt want debug mode running on a publicly reachable machine
