Whenever the nock end of a bare shaft flys any direction other than directly behind the point end, the shaft acts like a rudder on a sailboat. So when the nock flys low, the pressure of the air against the shaft creates an upward force, which will cause it to impact higher than a shaft that is flying with the nock directly behind the point. A fletched arrow quickly corrects this condition, so the nock low has little effect on the impact point of the fletched arrow. Which is why we would expect to see nock low bare shafts impact above fletched arrows.
The fact that you don't see this is interesting. It means that either your nock low bare shaft is a false nock low, or that something is causing your fletched arrows to deflect upward. I don't know what a false nock low would mean, as I have never seen one, but perhaps someone else has. I do know that if your nock point is really low, then you can see a bounce in your fletched arrows right after they leave the bow as they rebound off the shelf. Perhaps this bounce could cause a fletched arrow to impact higher than expected.
I'm assuming you have no significant fish-tailing?
After making sure that your arrow nocks are fitting properly, I would set your nock point at wherever it needs to be to get good bare shaft flight. If you aren't happy with the way it shoots at that nock point, then it may just be one of those bows that don't shoot well three under. I've had a couple of those that I've eventually traded to split finger shooters, who have had better luck with them.