This is a combination of empirical observations and the science though. As I have understood it the science predicts an air velocity in the port, but it is empirically observed that values of theoretical velocity in excess of a given value result in chuffing. It doesn't matter if the real values of air velocity in the port are way larger or smaller than the theoretical ones, just so long as they are related so the empirical determination works.
Actually the thing that surprises me most about chuffing is the crude aerodynamics of most ports I've seen. If worried about the phenomenon surely both ends of the ports should have well considered surfaces. I presume it's different in high end kit. Haven't examined any in detail.
Agree 100%. It is VERY cheap to add a aerodynamic flare/flange to a round port and it can make great improvements.