RE: Bare shaft tuning?
I do it occasionally. I haven't for while though. I did it on a Reflex bow I had because I was having problems getting a tune in it.
Basically, it eliminates the fletch contact from the equation. If you can get a perfect tear with a bare shaft, it makes it easier for the fletching to keep an arrow flying straight. Make sense?
Personally, I don't give paper tuning too much thought anymore. I do it, but only to get me close. Group tuning is answer.