Because it calculates the flow over throttle plate without taking pressure into account and thinks that the throttle opening is enough that it gives for your load request. The supercharger is always producing boost, even if your manifold pressure is below atmospheric. How much the throttle sees of that really depends how it's set up and when the recirculation valve opens.
You need a dyno and then move the throttle to each operating point and calculate the actual airmass (baking the supercharger boost into it), then populate the throttle map and inverse of it.
Setting all the maps to eleven is not going to do jack shit, better get really cosy with FUEDK.
Or you need to measure pre-throttle pressure and multiply the pre-throttle flow like with SY_TURBO...
screenshots below were my last attempt of exaggerating just to see how it went. i tried baking the supercharger boost into kfwdkmsn and kfmsnwdk, but honestly, it didnt change anything. my msdk will not change. is there a TB limiter that i am not seeing here? even logged wdkugd_w (which is what i understood the changes would reflect also, and it doesnt.)