My Xbox One S is part of the preview build/early update ring, but I don't remember seeing this preventing automatic updates. This goes for both system updates and game updates.
My console is set to Instant-On, I have the box checked to keep games & apps up-to-date, and my console is set to turn off after 6 hours of inactivity; I usually power off using the controller when I'm done though.
Any possible causes or would the preview updates necessarily explain everything?