[AlaricD]

I imagine that there would be pumping losses due to the higher dynamic compression ratio. Would, at certain loads, an engine with a higher compression ratio have more pumping losses than one the same size at a lower compression ratio? (For example, just tooling around a parking lot or in very light traffic.)

If this weren't true, then why would the supercharger be controlled by the ECU in the first place?

I suppose running at a certain amount of boost could cause the system to enrichen the mixture and possibly reduce the amount of spark advance to prevent predetonation. (Maybe water injection could help with that.)