I understand what you're saying about some magazines getting the car into the 11's but the same can be said about the Z06. For example, for the most part fox body mustangs were mid to low 14 second cars (assuming a decent driver, and a 5 speed). Muscle Mustangs and Fast Fords magazine on the other hand got a bone stock fox body into the 13's. It has to do with them making many many runs, trying different things (icing the intake, removing the sway bar, short belts, tire pressures, removing seats, power shifting, etc)
The same can be said about the Z06. Sure some of the main stream magazines will get it into the mid to high 11's, but if you put that car in the hands of a Vette magazine with some good drivers and alot of time you'll see much lower times.
Again the same can be said for the '03 Cobra. Sure MM&FF might be able to get a mid 12 out of it, but for the average driver who isnt going to beat the car to death trying to get that next tenth it isnt going to be that quick. Believe it or not i've seen guys run 14's in '03 cobra's while others like you said will spend the time testing and tuning to get it in the 12's.