At the end, he asks "What would a version control system for a web app look like?" Perhaps that's only a rhetorical question, but I think he's already touched

At the end, he asks "What would a version control system for a web app look like?" Perhaps that's only a rhetorical question, but I think he's already touched on a partial answer: it's a configuration management system. A good configuration management system will help you keep track of what's currently deployed where (although variation per login id is generally out of scope) and help you be sure that the requirements for deployment are met. The source for the configuration is normally kept under revision control for non-branch elements that revision control does well: why the change went in, who put the change it (in case the "why" was incomplete ;-}), what the change was (centralized diff), and when the change went in. When can be important for those little used but essential features that you find out stopped working some time ago, and you want to find out what made it break. He advises discipline in removing unused configurations. I'd like to hear what sort of dependency analysis tools support that activity.