probably is the cheap caliper set. Measure the same round 9 or 10 times and see if the calipers vary. If they don't, then there is something flexing or moving on the press. Check it out closely.
having the powder down against the bullet lets the primer ignite more cleanly and increases velocity without increasing the pressure within the case. You should try loading them upside down sometime. I find it will also tighten up the groups about 10percent over the primer down loading method.
I would suspect that you are not totally bottoming out the press when you pull the handle, or the die plate is moving or flexing at full stroke. Brass length has nothing to do with OAL and I doubt the is 5 to 7 thousandths difference in the depth the bullet is seating into the seating die. The...
Why would you neck size only in a bolt action? Sure, it gives better accuracy, but it makes it tough to chamber the next round, since the brass is fire formed to fit the chamber. I have neck sized only on 30 06, and can tell you that I wouldn't do that with any rounds I intended as hunting...