Even though a pellet is seated with it's centerline perfectly inline with the barrel CL, whats to guarantee that the pellet will emerge from the muzzel as loaded?
Just about every pellet I examine has a poor aspect ratio. Where the bearing points of the skirt and head are generally closer together than the caliber. That is asking for trouble especially when the pellet meets with a bit of debris in the barrel which can shift the ubstable nature of the pellet orientation within the barrel. Compressed air cannot deliver an even push to the pellet as, say, one might achieve by pushing the pellet thru the barrel with a flat fronted dowel.
Since the crown does not change from shot to shot, it has to be poor pellet loading or pellet interaction with the barrel which causes those sometime unexplained fliers.
Ask any machinist why his knees rattle and his butt quivers when he is tasked with pressing a bushing into a hole where the bushing has a poor aspect ratio ie larger in diameter than it is long. This is even troublsome under the best of conditions.
But we expect air, with it's inability to push with even force distribution to the pellet to run the gauntlet of the barrel.