Weight
Let's talk fact. Driver is the number one factor in any race. However, in the event that two drivers are equal, manuals just have too many advantages. First, off the line... I don't care how well you "power brake", it just ain't gonna beat a manual. Second, gear choice... Unless you have a special system, you just can't get the downshifts and upshift RPM's right. Last and most importantly weight... Ever wonder why manuals get better gas mileage when driven CORRECTLY and CONSERVATIVELY? Weight! I'm not going to act like I know the exact numbers cause I don't, maybe ya'll do. But automatic transmissions just way a couple hundred pounds more. So you have a lower power to weight ratio. So yes, mods will make up for the weight, but you just can't overcome the other two weaknesses...
Then again, tell that to Porche and its 911 turbo pullin a 3.4 zero to 60 with a triptronic automatic. Of course, manual is 3.2.... Why? WEIGHT!