Wrong.
Its all the same computer for 5 speeds and autos. It depends on the what "catch code" or tune you start with.
What matters is the tune in the computer's memory. The GT used a T4M0 tune, which was the A/F curve for a GT running 19 pound injectors. The Cobra used a J4J1 tune, which was the A/F curve for the cobra's better-breathing HCI and 24 pound injectors. The U4PO tune is a GT tune, but for an automatic with all of the slush box parameters in there.
I could have loaded the U4PO tune into my computer from 5 speed GT, slipped it into an automatic GT, and it would have run and shifted like stock.
When you run a TwEECer for the SN95, you have the ability to load the "base" of the above three tunes into your laptop and further modify them from there. 99% of people load the Cobra tune and modify, as the Cobra has much more in common with a modified car then the GT.
All three tunes work with the same physical computer.
I don't know Pete or his work, so I have no idea what he used or how he tuned it. It looks like you had a base tune for some prototype Cobra 5.0L. If Pete is as competent as you say then the "tune" that came with that computer has been wiped out, or bypassed, and Pete's tune imposed on the hardware.
Adam