I believe the issue with the stock bypass valve is that it vents back into the intake between the airflow meter and the turbo as opposed to out into the atmosphere. So were you to run something that vents to the atmosphere it would cause problems because it's subtracting air from the amount already measured by the AFM.

I guess in theory you could run some kinda aftermarket BOV and have it vent back into the intake like the stocker, but then you wouldn't get the waaa-pshh noise.