I have the same rattle on my 335i. From what I've read on various forums it looks like this flap is purely for noise reduction.
The flap actually remains closed if you are just idling or cruising with low RPMs. But once you press the pedal to the metal it opens.
I did the "unplug connector in the boot" version of the golf tee mod and noticed that the exhaust sounds a bit louder during regular driving. And I think I get more "pops" when decelerating.
Here's a good guide on how to do it (takes 2 minutes) to do:
www.e90post.com/forums/showthread.php?t=80661