BMS did further testing on a 2014 550i that had the stock exhaust pieces in place and the results below 4500 rpm were about the same. Above this RPM though the car without downpipes showed more power. The power once tuned however is about the same between the two.
Here is a Dynojet graph comparing a 2011 N63 based 550i and a 2014 N63TU based 550i both with stock downpipes. The N63TU shows a smoother torque curve and a good amount more torque especially from 2700 to 4500 rpm:
Here are the N63TU tuned values on the 550i with the stock downpipes (transmission shifting issues prevented dyno measurements before 4000 rpm from being picked up:
Here is the tuned N63TU with aftermarket downpipes from before showing slightly more torque although slightly less peak horsepower than the car without aftermarket downpipes:
What is the explanation? BMS states the factory ECU is reducing boost in both stock and tuned form above 5000 rpm. Why? That is anyone's guess. BMW seems to have designed to the ECU to reduce its boost target in that RPM range. It is going to take further tuning to eliminate this and at that point aftermarket downpipes should show gains but as of right now the ECU is reducing boost stock, tuned, downpipes, etc.