I'll try to explain this as best as I can. When you leasurely accelerate the supercharger isn't on. The ECU doesn't see the need as you are just putting along. Well you see the supercharger must turn on before 3,000 RPM because that is the way it is designed (belt load would be too high if engaged later). So once you get close to that RPM mark that clutch has to mate up or catch up with a rotating assembly that is spinning really damn fast. I don't know of anything that could make it a smoother transition.

Now like you were saying when you stab the throttle the engagement is almost non-existent. That's because a different scenario just happened. The ECU saw that you needed to get going in a hurry so it engaged the supercharger much sooner thus eliminating the need to "catch up" with the rest of the rotating assembly.

Bottom line? I try to stay away from that occurrence buy leaving it in D. Then when I put it in manual mode I change my driving technique to be more sudden. Understanding just how this car works and what to stay away from (such as this engagement) should keep you happy for many many more miles to come.