Here's a thought: Ignore most of the stuff you're thinking about it (too many variables), and concentrate on what's causing your initial problem.
Measure the neck diameter before trying to seat a bullet (in your case, brass as received.) Measure a neck diameter after seating (non-crushed case.) If the difference between the two is more than, say, 3 or 4 thousandths difference, the necks on the brass (as received) are too small (which would cause your crushing problem. It appears that way in your pics where there is a smaller diameter above the shoulder up to the point that the bullet base sits in the neck.) If that is the case, you'd need to open them up a bit (sizing die with expander ball but decapping pin removed will work. Run the cases deep enough to get the ball through the neck but not deep enough to resize the neck, then extract the ball the other way.)
Your bullets should measure .308" within about a half thousandth (because, well, it's a .308 bullet.) Adding 2 times the brass thickness (let's say a nominal .015") should bring you to just under .340" for a loaded round. If you assume the same .004" interference fit, your unseated neck exterior diameter should be in the .336" range (give or take, depending on actual interference, and actual neck wall thickness.)
Once you get that part verified, make sure your die is set up correctly.
For seating die setup, pull the seating stem way up into the die. Pull the die body up in the press. Place a piece of brass in the press, run it up, and screw the die down until it encounters resistance (which should be the crimp ring hitting the case mouth.) Unscrew the die about a half a turn to get the ring off the brass, and lock that in place. Lower the brass, place a bullet on the mouth and run it back up. You shouldn't feel any resistance doing so. Screw the seating plug down until you hit a stop (plug contacting bullet.) Lower the ram slightly and give the plug a turn or two of down. Raise the ram again, which will partially seat the bullet. Lower the ram and inspect how things are progressing. Repeat lowering the plug until you get to the length you want.
Note that brass will "fit" in a rifle or a case gauge even if it is way undersized in the neck or shoulder or body. Fit (or rather, lack thereof) will tell you if it's oversize, but not undersize.