SDS5: You describe this issue as "...outrageous... " - I think this characterization is grossly unreasonable. Cars are imperfect machines, and things necessarily do go wrong (even in $60K cars). It’s also worth noting that the S5 is in its FIRST model year, which is typically a period in which there are many growing pains. I knew I was bearing some risk in buying a first model year car on an entirely new platform. If this is the only widespread problem, I say congrats to Audi on a job well done. From the outside, this sounds to me like a bad batch of bearings from Audi's bearing supplier, not some systemic engineering flaw on Audi's part. Don't you think that the S5 underwent hundreds of thousands of miles of shakedown testing, and that they would have caught and fixed this if it was either a design flaw or that there were inadequate specs on the bearing that were causing premature wear or failure? I think so. If it is an overall engineering flaw, as evidenced by repeated failures in repaired cars, well, then we can start tossing around words like "outrageous."
I share your hesitation about having your (my) car be the first car torn apart for a transmission R&R, but this is where trust with the dealership comes in. I do know for a fact that they have a tech who went to S5 training, and I am confident that this tech will be the one working on my car. I'm not crazy about my car being the one he learns on, but that's life. Yes, the crank-diff-flywheel-clutch arrangement is unique to this car, but I feel like this will only enhance the diligence with which the tech will perform the repair. I'd also like to see the TSB, if it exists at the time, but I'm not going to pound the table for it.
"b) physically show me all the special tools that are required to do this job - those are the tools that the manual says that will be needed." Come on, you can't be serious... that is such an unrealistic demand. If I were a dealership, I'd ask you to go elsewhere because it sounds like you'd be the type of person who would be impossible to satisfy. Note also that this repair does not require removal of the engine.
I know your post was intended to be constructive and helpful, but I really think you have some unrealistic expectations about this situation. It's fine to be insistent that the dealer act with extra care and diligence in doing this repair, but you need to temper your expectations with a little easiness.