Okay, the auto trans thing makes sense to me. That way the PCM (controlling the auto) is on the same page as the ECM (controlling the engine).
I am curious as to what the rationale is for the re-clocking of the APPS is to fix the dead pedal syndrome. When you
look inside an APPS and see what is accomplished by the latest and greatest set of APPS "recalibration" directions, it would have nothing to do with the dead pedal or surging symptoms. Since the ECM will re-learn the new high and low voltages from the APPS the first time the accelerator pedal is pressed to the floor and released after turning the key on once the batteries are reconnected (per the service manual), you're pretty much right back to where you started. Walt's auto transmission explanation would justify the adjustment, though.
There are two different methods of "recalibrating" the APPS floating around on the TDR, and I think the purpose of each one has been blurred. The first (disconnect/reconnect the batteries, key on, depress/release the throttle) will "teach" the ECM the voltage range of the APPS. The second (the newly discovered re-clocking method), as Walt has pointed out, will sync the PCM and ECM throttle readings to make the auto transmission shift correctly. The first method may fix a dead pedal (if the ECM completely forgot the voltage range of the APPS), and the second method has nothing to do with those symptoms.
Of course, if I'm missing something, someone please fill me in. But, imo, it seems that this new method of re-clocking the APPS is pointless unless you're trying to fix a shifting problem in an auto.