The contoller, in effect, splits the load between the two cp3's. Reality is, the controller just duplicates the signal from the ecm. The ecm has no idea more than one is present. So, the ecm actualy does the control. The ecm, in effect, sees the one cp3 able to do the work but at half the duty cycle ( depending on how you view it, on or off ). Hope this makes since.
Of course this is my take watching it with a scope.
Then why the scare of running them on a stock motor? If the ECM still only commands "X" psi then how does it produce harmful pressure? I know this ventures into the engine arena but if the electronics call for 29,xxx then why ?