How about taking the approach of the browser on android 4+? The top bar disappears as you scroll down, but pops into view when you scroll up. It is then aligned

How about taking the approach of the browser on android 4+? The top bar disappears as you scroll down, but pops into view when you scroll up. It is then aligned with the user's intention, a scroll up being a signal that they wish to go up to the menu. Combine with a reasonably speedy fade-out for cases where a user is simply scrolling up to re-read something, and I think it puts most of the usability issues to rest.