Kraut, I do not know what all ECM mods might be done, but do know that RevPerf has 1000's of maps for 100's of different motor configs built over the years, and they are dyno tested (info direct for RevPerf). I know that a map load with as close to your particular setup is done. Beyond that, not sure, but there are apparently some adjustments in the Delphi units that allow RevPerf to optimize the inputs from their add-on tuner box and widebands for the tune.
The critical piece, according to Brian and his engineer I spoke with, is the injector. If its changed out, the ECM will need to be sent in to be updated. So, I presume the accurate fuel pulse width/timing is what they are likely making either more efficient or more accurate. This would make sense, since the EMS box plugs between the O2 lines and the wideband O2's that come in the kit. I presume there is very precise O2 readings taken and fed back to the ECM for the AF/MAP/VE calcs and adjustments.
Again, this is a guess, as it is proprietary whatever it is they do.
Dennis