I have only noticed it on the upshift, but you also get to hear it make a little burble on the efficiency mode when the power goes off when it goes into coasting downhill.
You can also amend the level of noise from the MMI, not sure which parts this turns off. I have this setting on individual mode so I can has the sporting steering and accelarion but not the louder noise.
I am guessing the attenuator (speaker) and the exhaust flaps are available on both manual and Stronic S3s, and more for normal engine sound not just the gear change sound.