Cobb did address this question somewhat on their website. They say it is safe to run the Stage 3 tune with a stock CBE, as long as you have all the other parts installed. As for power, I don't think anyone has dynoed their car back to back with stock and aftermarket CBE to say for absolute certain. I'd wager that if it is safe to run the Stage 3 tune without a CBE, then the power losses would likely be very minimal since the stock CBE creating excessive backpressure would make the tune unsafe. Just some armchair analysis.
Also if you are just trying to be stealthy but really want to make sure you are getting every last horse, check out clips of the Milltek resonated exhaust. It sounds extremely close to stock.