Lots of good questions and ideas here. Im a stickler for a clean bore, Im certain there is no copper staying in the bore, its spotless. Overkill is underrated so I hogged out the barrel channel more than was necessary, barrel shouldnt be able to contact the stock under any conditions.
I always weigh sort my bullets to the 1/10 gr. For testing 165 gr SSTs, every bullet I use will be 165.2 or 165.3 I always choose to load ladder test with bullets it always the same or no more than 1/10 of a gain off from the others just to eliminate another variable. I wont run some that 164.9gr with those that weigh165.5, even though I imagine it won't make a bit of difference especially it only 100 yards, but I do it anyway because Im OCD and a perfectionist. I will never be able to load fast but it is what it is.
I've tried this with CCI 200s, Winchester large rifle primers, Winchester large rifle match, and S&B large rifle primers. Anytime I do a load work up, all the cases get primers from the same batch, I never mix different primers in a test.
I do have multiple scales that I check each other against as well as calibrate them frequently. I'm pretty sure I've got this issue nailed down to 2 problems. One is I may be slightly over annealing, resulting in inconsistent neck tension. 2nd issue I believe is thinning necks from having varying numbers of loads on any particular case.