It shouldn't be different. There is nothing measuring manifold or boost pressure on our cars. The ECU isn't targeting a certain pressure, but instead should be going for an airflow target, based on throttle, rpm, temp, load, etc. If there is more airflow than expected, it opens the wastegate some, or vice versa.
AFAIK, the ECU calculates boost pressure in a similar way that a MAP car calculates airflow, just going through the VE equations in the opposite direction. Since VE changes when you do things like add a different turbo, free flowing exhaust, FMIC, whatever, that's why you see guys reporting different levels of boost when they make those changes. The ECU doesn't know that you just changed VE, and so it goes to targeting it's normal airflow.
Although extending that, if VE goes up, airflow goes up at a given boost, so you would suspect pressure would go down when following that scheme, when most report the opposite. Hrm. Time to really figure out what the ECU is up to here.