low speed + low boost, = poorer cylinder filling. 'swirling' helps the filling part, think of hammering a square peg into a round hole. when the air charge is 'spun' into the cylinder, it helps 'fill' the dead corners. The harmonics of impulses within the plenum all the way through to the top of the piston is a pretty complex dynamic.
You're correct, 'hogging' out a port tends to hamper low end..
But when you have choked down runners, they tend to really speed up charge flow, which actually helps the cause.. up to a certain point... but eventually will be a limiting factor after a certain CFM.
Think of a funnel. Have you ever noticed sometimes when filling a gas tank while using a funnel, that sometimes the fluid will 'swirl' down the funnel? (and quite fast too) But the next time it might just fill up and 'glug-glug'..
When dealing with NA engines, a system could be designed around the amount of air expected to flow. Now when dealing with engines that can run anywhere from zero boost, up to (insert your boost here) It gets complicated on dialing in the 'perfect' setup, one that suits both low end, and wot operation.