Actually, stock versus stock, an auto turbo mkIII will beat a 5-speed every time. The 0-60 time for the mkIII auto was 6.2 and the 5-speed was 6.5 to 6.7 depending on which magazine you believe. Of course you have to power brake the hell out of the auto, but with a good launch and the lockup torque converter, the auto wins...why you ask before you flame me? The auto never has to let off between shifts so it never looses boost. Everytime you shift the 5-speed, you loose boost and have to build it again.

The 300ZX TT had the same problem so nissan actually de-rated the hp of the auto down to 280 while the manual got 300. Even with this change, the auto still beat the manual to 60 and in the 1/4 mile by a few tenths.

Now to answer your question, no a supra can't run 12's on a ct-26 even if it was upgraded whether it's auto or manual.