As many have found the very cost effective LEE shell holders are a little varied in dimensional differences compared to other brands. I have not actually measured myself, I do intend to, but my buddies have mentioned it. On straight wall cases this makes no difference at all.
However on "necked" cases this can effect the distance the shoulder is pushed back during forming or resizing. I loaded a very few of the .401 GNR's last week and they will not fully seat in my chambers. Pooh. I know the die was bottomed on the holder when I adjusted it. In the past I have adjusted my sizer dies by turning in a lathe to shorten the die body a little to suit. Not something everyone can manage. But the shellholder makes more sense to shorten by turning or grinding. They are cheap and if you mess it up it's not a great expense compared to a die in a custom set.
It's always good to have the gun or cylinder at the loading bench to ensure no issues at a later time. Make sure the empty brass fully seats in the cylinder. Loaded ammo too, it may have bullet issues related to seating. FWIW