Unlike carbureted ITBs, injected ITB does not draw a premixed air/fuel, the "extra cylinder charge" in the EFI setup will be a given amount of fuel plus extra air rammed in at tuned rpm. If the velocity stacks offset the difference in length, then the wave paths will be the same. Your argument is that with less than half throttle, the wave bounces off the throttle plate, causing the wave paths to be different again, that is an excellent point.
I think with the throttle plate nearly closed, the wave path is cut even shorter so the harmonics is going to happen at even higher rpm(higher than 6800rpm). Since the effect of different wave path only happens at higher than 6800(which is beyond the point of max hp) AND less than half throttle, the scenario is not involved in power making and doesn't really matter in this case. That's just my theory.