TommyBear,
project settings will only write to your personal local run-time generated INI file, which means that those settings will only apply when running project directly from your local folder. When you package your project, your local run-time settings will be ignored, and only project’s default settings will be used.
To make your personal settings default for your project, please click “Save as default” button. DefaultEngine.ini file that is included in your packaged project should then have desired startup maps.
I will make a usability pass on Settings UI this week to make distinction between personal settings and project default settings, as well as their relationship to project packaging more clear. Sorry for confusion!