Skirt diameter, skirt pocket, thickness of the skirt, head diameter , shape, weight, material properties... It all plays a roll. Plus once the pellet leaves the barrel then there's the aero dynamics.
Take the JSB diabolo, H&N FTT, CPH, and Barracuda match all are very good quality dome pellets and even at when I have 4.52 head diameter they fit the barrel a little more or less snug as the other. And you are correct in your observation that internal pocket of those skirts are noticeably different in each.
The good news is usually one of them are consistantly accurate.
I suppose that all the minute variables in the pellets is what makes up for the barrel variations as well.