Agree completely. This should be front-and-centre in the documentation. A CMS built on top of Django should, by default, be just another Django reusable app. It shouldn't take over your entire project.
The `mezzanine-project myproject` bootstrapping command should be just an optional shortcut for projects which are completely CMS-based. Which, in my experience, is the minority of projects.
Mezzanine provides a platform that allows you to do a lot more than just CMS stuff, so some projects aren't completely CMS-based. The mezzanine-project command just creates a django project that has some settings already configured (installed_apps, middleware, urls, etc...) so you definitely could integrate Mezzanine into an existing project. In reality Mezzanine is a Django reusable app.
The `mezzanine-project myproject` bootstrapping command should be just an optional shortcut for projects which are completely CMS-based. Which, in my experience, is the minority of projects.