Thanks for the screenshot - very helpful.
What's happening is that the checkbox you are selecting simply makes sure that the CMS is built. If that checkbox is not selected, the CMS will not be included with your site.
The checkbox i am referring to is "Use as a content management template" which is available when you click Define next to the Site Type menu and you will see the option at the bottom of the next UI. Here's a screenshot of what you are looking for: ss-01.png