@skiptowncat have you looked at that self-study guide. There's a graph in there that implies that control of the bypass valve is not a simple as you suggest.
My point about the tuning box is that it only taps into the charge pressure and crank sensor (which I assume is only to measure rpm). So by sending signals to the ECU which are less than the actual pressure, the box can fool the ECU into allowing the boost to be higher. However the ECU thinks it is lower and so will calculate lower air mass and hence fuel for less air than is really entering the engine. To me it appears that with such a tuning box the V6T would run lean.