A true standalone engine management system would replace the stock PCM. Its a pretty daunting task to take away ALL the parameters the PCM controls since it has inputto everything from injector pulse to the alarm and door locks. However the systems they are referring to would give a more modified car control and a high level of adjustability on everything from injector pulse length, width, timing advance, retard, tuning by throttle position/load etc. I believe AEM was developing one. Currently most tuners use Piggyback systems which modify the signals associated with the stock PCM, so the stock PCM in a way is still the limiting factor.