Are you talking WOT or partial throttle?
FWIW, if the same systems are enabled/disabled between the tunes, you shouldn't see any difference. The SC head unit is still going to produce the same amount of boost at a given rpm, regardless of the tune.
However, the boost seen at the intake manifold CAN be affected by what other emmission control systems are enabled. For example, if the egr valve is open, you could loose some boost through the egr tune into the exhaust.
I've used several tunes, and never had boost affected by the tune (of course, assuming you are talking about the same boost at any given rpm). And as mentioned, part throttle vs wide-open can make a difference.