The intake will definitely cause Turbo/Bypass Valve sounds to become much louder. The SPT
should be ok, but I personally would stick with the stock intake with the silencer removed (optional) as it will be safer until you get tuned. Ed had the SPT intake fall off during a dirt drive which caused the death of his stock motor and it was starting to come off on his new motor too so he went back to the stock intake. He said the car performed much better on the stock intake and now he said he'll never use that intake again.
Usually it's only an issue that results from adding a more free flowing exhaust, but it could be wastegate flutter.
http://www.scoobymods.com/forums/showthread.php?t=3654