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I've had my 06 A6 tuned by Chuck CoW. It's by far the best mod you could do. The difference in shifting is very noticeable and it makes using the steering wheel shifter paddles more fun.
Yes, I usually update the 06/07 cars with the 08 GM operating system.
In addition to that, My A6 calibration is truly amazing. Not only does it have the power maximized, but the trans is ALWAYS in the right gear at the right time and unlike other (GM or otherwise) tunes it VERY EASILY backshifts with light throttle to what ever gear is most appropriate for how you are driving at the moment.