I'll cut to the chase and then provide my support. Nothing is "wrong". You and the factory are doing things "by the book". The end
but there is always "more".
I have 4 Nosler variants from 2014 on. They are "My version" because I didn't have to conform to "Factory rules" when specifying my reamers. 277/26-Nosler, 28 Nosler, 308/26-Nolser and 338/26-Nosler. I just recovered my original designs from the computer I was using back in 2014 when I did them. I did "paper" experiments from .243 to .375 but only built the 4 so far.
I provided that because I have probably a thousand or so rounds down range and 2 elk with them. Add to that the bench rest 300 RUM and ELR games 338/300 RUM and I am familiar with the behaviors of these types magnums. BTW: It would be more rounds down range but I am just returning to shooting after being away from it for 6 years track riding motorcycles.
back to the problem at had...
I remember seeing this before, mostly in these "Ultra Magnum" type setups. It's not a "problem" per say, it is an indicator of factory "error on the safe side", meaning. it's not really and error or problem at all. Your handloads on new brass duplicating the behavior falls in the same category.
Those that suggest "measure your chamber". There is some validity to that but it will not indicate any "problem", don't worry about that. If there were a real problem there it would show as something else.
Looking at your unfired, is it factory? and fired.
My belief based on pictures, description and information provided agrees with
@Rflshootr.
The primer pocket has a nice champher to it. Based on the pictures of the primers, it is what I expected.
There are no excessive pressure indicators in the pictures. Pictures can be deceiving but I don't think this is the case.
There is high speed videos of what is going on so
@Rflshootr is not conjecturing on the process. During the firing process, the ejector is holding the brass away from the bolt face, the pin strikes the primer and the ignition process begins. The primer backs out a few thousandths, then the brass expands to fill the chamber pushing the cartridge head back against the bolt face. The primer is "under pressure" so does no go back into the pocket and instead "mushrooms" a little. No problem.
If it were me, and it was back when...
Measure fired brass after punching the primer with just a decapper. As described by
@Rflshootr, this will indicate that you probably want to "bump shoulder" less.
Make up a couple rounds with this now slightly longer case and see if the behavior goes away.