All these things are just generalities right now...basing fact on a few magazine tests with test mule cars (a small sample size at that) will not give you absolute truth. I would say the auto is several mph slower, but is it almost 4mph slower...time will tell. I can tell you this though, a A6 with a small stall will be quicker AND easier on the drivetrain the vast majority of the time whether on the street or track. Granted it will not be as good for road course events, but as far as drag racing goes, it will end up being a very capable setup.
Once folks get rolling with the VVT cam research, I think you will see the playing field start to even up on power output (once AFM is removed). Even though the peak numbers may continue to be lower on the L99 the AUC power produced by the VVT technology along with a stall converter will create a vehicle that will ET awesome in the 1/4, albeit at likely a lower mph. Remember, peak #'s don't necessarily mean it will be quicker, having a large AUC with a flat TQ curve, means these heavy pigs will get rolling quick...factor in the STR of the converter and they'll leave the line in a hurry on DR's. A 6sp manual will do it also, but you'll have to clutch dump it to 60' with the stalled auto and that is neither clutch friendly nor rear end friendly.