The issue is that unless you have standards such as directory locations and structure, users and permissions, there isn't a way to automate the process of code deployment even with chef/puppet.

PaaS works because the provider has a standard and forces you to follow them. I don't mean that in any negative sense. I was in SCM for a number of years and know that kind of enforcement is necessary if you want to have any kind of repeatable, automatable and supportable deployments.