Brake control compatibility with exhaust brake

You want a momentum based controller regardless of anything else. Timer based controllers are inferior in many ways.
The momentum controller doesn't care what is slowing your truck: brakes, exhaust brake, downshifting, etc. It just knows it's slowing and how fast it's decelerating. It will then apply your trailer brakes accordingly. Prodigy seems to be a favorite for many. I have the Tekonsha Primus and am quite happy with it.