With a choke rather than a smooth bore, you are still compressing the shot, even inside the wad, at the last 3" of the barrel. This last effort of compression tightens the wad and the shot as it leaves the barrel and therefore results in a tighter pattern during flight.
What I wrote above was nothing more than an educated guess. I think many will agree that there is no scientiffic data or theory to explain exactly how a choke works. If there was, then all choke manufacturers could make their products to exact specifications and all would work relatively the same.
Choke making however, is not a science, but an art and some chokes just work better then others.
