I think you're overthinking it.
A) You get good fletched flight.
B) Bareshafts group with, or slightly weak to, your fletched shafts
That's all you're interested in! Move your nock back up to eliminate the shelf wear (although this really isn't a problem) & leave it at that.
You seem to be mixing 2 different tuning methods (actually, I read this a lot) You need to either go with the 'planing' method of O.L.s or arrow nock position, not both. If your arrows are grouping together, both bare & fletched, then you're good to go. With O.L.'s method, nock height would be indicated by your bareshfts grouping eiter high or low.