It only makes senst to tune the bow to the way you shoot it.
As for bare shaft, there are several ways and they can work. O.L has a good guide for this at
www.bowmaker.net. Watching the nock location can give a bad reading. The target can have soft areas that allow the shaft to give false readings, as it follows the path of least resistance.
Shooting an arrow at longer distances and watching the flight can show you lots about how well you are tuned. Don't be afraid to think outside the box,experiment and see what happens.
Try diferent things, move the nock point and see what happens, after all it is easy to put it back if things get worse.
Try a diferent point weight and see what the result is. It is easy to change points and confirm the shaft is weak or stiff, but after it is cut it is to late to go back.
I helped a guy tune his bow one day and his flight improved greatly by using a 250 gr point.
This gave him 2 options, change point weight $3.00, BH adapters $12.00 or shorten the sahft. There was no way he would change weight, as he already had points and broadheads, and he insisted the shaft had to be the length it was. He spent $80.00 for more shafts with a diferent spine and still ended up with so so arrow flight but he had 125 gr points and a 29" arrow and spent $80.00.
Thinking outside the box is good, and tuning is easy if we allow changes to happen. It is easy to adjust for a diferent trajectory , but there is no way to adjust for poor flight.
It is just a stick and string,nothing is complicated about it.When it doesn't work right change something and see if it gets better or worse. You can always go back to where it was.
Stick a twig behind the shelf/rest pad, move the nock, twist the string,change the points, it is all reversable and cheap or free to do.
You learn more from experimenting than by reading.
Pete