I assume by "natural supercharging" you mean achieving volumetric efficiency above 100% at a certain point(s) in the rev band. I would think that this phenomenon is a much stronger function of runner geometry than amount of cylinders, since this effect comes from pressure pulses caused by the resonance of the runners.
As for the main topic, I would think that the V12 would be at a disadvantage in terms of the frictional losses already mentioned. At some point, having more cylinders will give diminishing returns.