Yeah, the problem with autos is the gear ratio selection. It becomes less of a problem with big power cars. But you're starting with a ****ty 1st gear, and only using 2 shifts to get to your 1:1, so the ratios must be wider spaced. A 5spd car has a much better 1st gear, and each gear is closer ratio considering they are spread out over 4 gears (you don't use O/D on the track). I've seen a comparison where they took an 11sec fox with a pretty nasty built 4k stall c4, ran it at the track, then swapped to a pro-shifted tremec 3550 without changing anything else, and went 3 tenths and 4mph faster. I'm not saying this will always be the case, but a properly setup and driven 5spd in a mild car will almost always be faster. But, all that being said, it also depends on the setup. A c4 will almost always be faster in a turbo car because of the same reasons. The ratios keep more load for the turbo to spool against, and make the shifts smoother keeping it in the boost. I'd like to see a comparison with a properly shifted stick in a turbo car though, because most people granny shift turbo cars, which is probably why they fall out of boost and are slower.
Anyone doubts an auto car, look at rsw007 and what he has done with an AOD. He is going about as fast as the good stick drivers with a bolt on car. He has since stepped up to better heads, but had been 12.8s on stock E7s. I have seen some 5-speed cars in the 12.5-12.7s on stock long blocks, and they all have been sticks, but auto cars can do it as well. Another note worth mentioning and Blackened can back this up. Grabbing second gear right after your bumper nearly hits the ground, and having the car hang the front tires through half of 2nd is simply bada$$. Not to mention a 9 or 10 second stick car going down the track is a thing of beauty.
You guys are forgeting the drive differances between an automatic and a manual. Clutch has less slipage and will "lock up" instantly,but- a torque converter multiplies the engines torque,so the transmission will see more torque behind a torque converter than a clutch,hence the reason for the lower gear ratio in the automatic,it also slips more so the engine will rise in RPMs faster.