I too have given this some thought, and came to the same conclusion as you regarding the flairing out of the pellet skirt, so I decided to conduct a little experiment. I loaded a few mags up with some perfect, and some deformed skirt pellets (noting where each one was), then fired them at a target. All I can say, is that I did see a pattern of inaccuracy with the deformed pellets, as opposed to the ones that looked right.
My solution? I bought a pellet sizer for £18 off that well known auction site. Any pellets that look misshapen, I put them through the sizer, it not only sizes the head of the pellet, it also reshapes the skirt into it's original state.
Sorted!