Correct! And if you notice Power Commander 3 and 5 give you the ability to programm or build your own MAP since they take in a signal from the Throttle Postion Sensor(TPS), which has to calibrated to the throttle valve on-the fly piggy backs don't do. In this case of building your own fuel MAP, it will be contingent on if the pink was cut or not when you built it since the PC module was seeing the voltage from the stock ECM when built. PC offers a few different base MAPS on their site for download if you don't want to go to the dyno, one can try use your plugs as a guide w/ any piggy back to fine tune. PC does not say "cut pink" on the site and offers a stock MAP download, so assume they work with it not cut and/or one could experiement with any piggy back to gain different fuel MAPs.
The ECM and piggy back are based on tabulated values they read to determine fuel delivery. In the case of the ECM, inputs from sensors of different SI units. In the case of on-the-fly piggy backs, fuel voltage frequencies from the ECM to the injector are read and some percentage above that voltage to add voltage/fuel depending on the setting. In the case of PC; ECM fuel & TPS, and in the case of the PC 5 autotune, additonal O2 sensor or oxygen level voltage input that senses load on the motor by how efficent fuel is being consumed or burnt.
As of today we are hearing rumor that the 2010-2011 ECM removed the pink MAP due to EPA emmissions violations, but left the wire intact. Nothing has been confirmed, if you own one you could do voltage checks to see if cutting the pink matters.
The stock and pink MAPS are two different stock ECM fuel MAPS, a "Race ECM" does not add more or change them, it just removes the "limp mode", a mode to protect the motor in the case of overheat. Word is some engine builders have the ability to reprogramm the ECM eliminating the need for the stock MAPS or piggy back with MODS. Check with them.