It all has to do with the stiff side of the arrow being against the bow. If the arrow is tuned properly for your bow and your style of shooting the fletching shouldn't bump against the bow with the cock feather in or out.
I don't get the part of "shouldn't bump against the bow" I thought that if the fletch hit the riser it would deflect. 
On another note I was reading a good article and the bowyer takes say 20 freshly made arrows and shoots them. The arrows that don't make the cut get thrown away. On average maybe only 4-7 arrows make the cut out of 10. This makes sense becasue not all wood arrows are created equal, the grain is never consistent.
Having said that if I cannot tweak the arrow I'll scrap it... 
If you just use whatever dowels you can find, that might be the case. If you are purchasing matched shafting, you may end up with one that just seems wonky....if you are prone to bad luck.
Matched shafts will vary slightly in mass and stiffness, minimizing variation in flight. On top of that, if you bare shaft test the arrows before fletching, you can trim all the arrows to optimum length and further reduce variation in flight. But trying to do that with unmatched arrow shafts is like trying to race a horse with four different sized legs!
