For an app I'm working on, we've decided to by-pass the default AEM Mobile nav and status bar and use our own menu/nav system. Under "Content & Layouts" > "Font & App Customization", I've selected "Always Hidden" for the navigation and status bars for both phone and tablet.
However, when I load the content in preflight, the nav bar is still appearing on the "home screen" (article page we've designated as the first screen users will encounter with navigation links).
We do have two collections on the top level to keep content organized (though we aren't showing them as collections)--could that be the issue? Is this just a preflight bug? Is there any other way to make sure the AEM Mobile nav doesn't appear?
OK - that would explain why you are still seeing the menu bar etc. The preflight app that you download from the App Store will not show app customizations or fonts etc. Test test this out, you should consider building an app in the portal and enabling it for preflight. Here is a chart that shows what the public preflight app supports vs. a custom app etc.