Here's some ideas for a lower profile rotary encoder knob. See if this helps with the overall design especially center mounted. You may have to use a spacer to offset the rotary encoder or source a different one:
http://www.adafruit.com/images/970x7...G7UI6cXMfT.jpg
http://www.robot-italy.com/media/cat.../0/2055-02.jpg
Unfortunately, it'll be difficult to make space for a boost control module unless you put the rotary encoder on the extreme sides. Heck, maybe it can be an option with detachable face plates.