Thanks for the link, that's a very good document. I think it may take 2 or 3 reads before it all sinks in but a really good reference point.
The one thing It doesn't appear to address is my original point about all six inlet tracts are on the same side of the engine. So as this is a VR6, 3 of the inlet ports are several inches further into the cylinder head so this must affect the flow, the pressure waves and VE relative to the opposite cylinder bank.
It doesn't matter what the variable intake is doing as you can't satisfy both requirements for any one engine speed?