Different people have different opinions about this, but my opinion is that you can get meaningful results from bare shaft tuning as long as you have consistent form, draw length and release. HOWEVER, you can STILL get meaningful results from bare shaft tuning even if you're NOT always consistent as long as you KNOW when you're not consistent, so you can ignore those shots.
Similarly with the two best known methods of bare shaft tuning. The method where you observe where groups of bare shafts impact the target is probably the best method. However, if you don't shoot well enough to reliably group bare shafts, the other method where you observe the bare shaft flight for nock orientation is perfectly fine as long as long as you know when you've made a bad shot and ignore that one. I am able to reliably group bare shaft impact points at 10 yards, but I still prefer observing the bare shaft flight for nock orientation because I don't like having more than one bare shaft for each type of arrow I shoot.
If you observe nock orientation in the target rather than when in flight, make sure that your target is not made of some type of material that changes the angle of the bare shaft when it hits the target.