I usually shoot through paper to check nocking point height. Other than that, it can be useful to see if somehting weird is going on like an arrow hitting a rest, hand torque, poor spine, cam timing or another problem. In my opinion, it has no place in determining final positon of nocking point and rest windage. Group tuning at long distances is best for that. I use to occassionally spine test with bare shaft tuning, but since I've started using a homemade spine tester, I've found bareshaft tuning to be unnecessary.

Why change your nock point? If your nock point is correct wouldn't you adjust your rest up or down? I shoot a release and my nock point is set an arrow width, approximately 5/16, above where a horizontal arrow and /or line intersects the bow string. Is This Not Correct?

The bareshaft arrows are going to have an increased FOC due to the lack of weight on the back of the arrow. Also, no fletchings to help them flying straight and level. Therefore, the bareshafts will nosedive a little and impact below the fletched arrows. If they don't, adjust the rest or nocking point until they do.