On my Boyue (awesome device, cut down before it's prime!), I used Xposed with GravityBox (JB edition) to put the reader in expanded desktop mode. I set it to not have any navigation or status bars. I then used GB to set the back button so that a double-tap took me home, and a long press brought up the status/navigation menu. This eliminated the black bars in all the apps I used.
Since the Boyue and your Onyx come from the same stock, perhaps this method will work for you too.
I messed around setting up pie controls for navigation, but due to the beveled edge, this was a little difficult to perform, so i abandon that and just stuck with button control.
It sucks about the slightly crooked screen, I can see how that can be annoying, hopefully you can get it replaced. Just make sure you get a case on that bad boy, that screen is fragile!
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