I have noticed that with some bows that once I get rid of the nock high while bare shafting the feathers are making a lot of contact once I use fletched shafts. Sometimes so much that the bottom hen feather is hitting my hand. Further, again with some bows, once I get the nock point low enough to correct the bare shaft nock high I am getting a tiny bit of shaft rub on the shelf of the bow -- and that is not good for consistent shooting.
So, I re-tune to get a little bit of nock high with the bare shafts and then check for feather and shaft contact with a fletched shaft. It is an issue of balance to get the perfect compromise for that particular bow, but if I get it just right there is minimal feather wear, no shelf contact and absolutely perfect fletched arrow flight.
In this way, the bare shaft tune for nock height is like that for weak/stiff. For weak/stiff the fletching adds weight to the rear of the shaft and thus stiffens the dynamic spine -- compensating for this with a slightly weak bare shaft works out very well. Likewise, the fletching adds size to the rear of the shaft and it is sometime wise (again depending on the individual bow) to compensate for this addition by bare shafting slightly nock high.
Just my 2 cents worth based on my experiences.