AppBuilder companion app is a separate app used as a "shell" that wraps up user's application in order to give a quick review on device. This way you don't need provisioning profile to test your app. By default companion app does not represents your app. You have to deploy it manually using our Build functionality.
Basically this is a testing tool that has some limitations
and you will not be able to use it for publishing.
Our Telerik platform provides a tool that eases apps distribution that you may want trying - AppManager
Check out the Telerik Platform - the only platform that combines a rich set of UI tools with powerful cloud services to develop web, hybrid and native mobile apps.