It's true with overlap and boost you can flush the boost out of the exhaust. At mid RPM and high compressor efficiency I think there is some boost to waste on this.
I'm still wondering when the fueling (injector opening) begins relative to intake cam opening. I'm pretty sure the fuel is not pooled behind the valve before it opens. I need to check with someone on when the injector is open, it's going to be on the downward induction stroke.