Anyone correct me if I'm wrong here but here's my understanding of the problem.
As the piston slides over the intake windows it partially blocks the windows. The air coming in through the intake is moving at a high velocity and doesn't want to stop. When the piston blocks the windows the air charge wants somewhere to go. Because those ports are always open to a volume (the tranfers) the incoming air charge, with sufficient speed, can shoot down there to fill the crankcase a little more. When the incoming intake charge doesn't have to start and stop again to keep flowing in through the reeds it means that the charge comes in faster than without the ports.