The Automatic PCM contains the TCM also. It is a higher cost item. The 5 speed PCM doesn't have the control circuitry (TCM) needed for the auto.
You are correct in saying that the auto contains 2 computers as opposed to the 1 in the manual. Prior to the 2003 model, the TCM was a separate controller mounted outside the PCM.
The current (2003) and later PCMs are called NGC for Next Generation Controllers. Combining the TCM with the PCM was one of the major changes they brought about.
Ian, you are right to pick up on the quick learn proceedure on the new PCM pointing to the extra computer withing it on the auto.
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