Your thinking is definitely on the right track & the flow theory is sound. However you are a bit flawed your basis.
The stock manifold setup was designed for a 170HP engine and the fact it would be primarily mated to a slushbox. Also the UIM was a compromise to fit under the stock hood. (It was EH'd for moderate flow improvement and port uniformity for the SVT)
Now about the IMRC. The rpm range of "just the short runners" drops drastically as you improve the efficiency of the engine and attached parts. (i.e. mods) The more modified the engine is beyond the stock 170HP slushbox range the lower the maximum rpm range of the short runners will be. There comes a point where the rpm range of the short runners is below even cruising range. Albeit, like you said, not on the stock engine or one close to stock. This rule of flow dynamics is part of the reason why an SVT has a 400-600rpm lower IMRC point even though the engine has a higher powerband due to the cam change. At a lower RPM point it needs more air then "just the short runners" can supply. That's even considering the bit of flow improvement the EH process added to the short runners.
