Darin Morgan has some posts on Speed Talk where he discusses the difference between sub-6500 rpm engines (most of our stuff) and high speed engines. Sub-6500 rpm motors will never get near the 124% VE maximum because there is not enough energy in the pressure waves in the intake tract to be able to pressure wave tune (and ram charge) the intake system. There is some inertia based ramming at these low rpm's, but not much pressure wave ramming.
As far as the velocity, the 640 fps (or 690) is the actual velocity of the air or air/fuel mixture in the actual running engine when 'choke' occurs. This is the point where further increases in velocity do not bring a corresponding increase in power. In other words, at speeds above 690 fps the engine looses more power from pumping losses than is gains from extra intake flow. This 690 fps would require a much higher differential pressure through the intake tract than the 28" that the flow bench provides. So, at 28" of differential (on the flow bench) 350 fps average velocity is the maximum possible. In a running engine much higher velocities will occur because the pressure differential can be much higher.