My Goat is at the Dealer for the my Third Dana Diff (axle assembly) . The whine that I've had sounds like a failing fuel pump. The first occured on accel from 45-55 but not on decel , the second was same but also at the 80-85 cruise. I was able to hear the whine until I turned the CD volume above 30. No one has told me want the cause is , they ride in it and order a new one. The First took 3 months to arrive , the second took 2 months . As far a performance I'd say that yes it does have a negative effect. I don't track so no numbers but from the Dyno tune I had done , I feel the RW numbers were down. With an A4 , I quess 15% is normal loss from Crank hP to RW hp , mine was more with the whining diff. To each his own , but this issue should have generated a recall.
If this Third Diff goes , I can say hello to Lemon Laws . The Dealership is spending more time this install - I pushed to have the rearend cradle tool used to check alignment and they are using it to check rear cradle alignment prior to replacing another Sealed LSD. Time will tell...
My Goat is a blast to drive and my daily driver - the rearend whine has been the only problem - but a drag of a problem...
Edit:
Mileage wise : first started whining at +- 4000 , second at 11,000 , I/m at 20,000 miles at dealership. Took about 3500 miles +- between replacement and whine reappearance.