You are asking to compare apples and turkeys. Two different calibers, two different cases, two different chambers.
Neck length isn't a huge issue in accuracy in my experience, as long as there is enough of it to hold the bullet. I mean is there really a significant accuracy difference between the 243 Win and the 6mm Rem?
Before I pontificate on which cartridge should get a premium seating die, why don't you experiment with your rifles, and see if you can figure out which chamber is more tolerant of runout?