I have plenty of spent mil brass, small base dies works best for me, I try to recover what I can and keep it in the same lots.
Your right about working the brass with a small base die, and maybe even some have not taken the press to the bottom of the stroke or are out of adjustment. I have to keep an eye on over lengths on these cases.
I have seen some rifle chambers that have to use a small base die on, even bolt guns can be this way, if they are tight chambers. Once fire formed cases only need neck sizing on bolt guns. I do not expect accuracy as near as good on my semi autos when compared to my bolt guns.
I tend to think a lot can go back to the tooling when the any rifle rifle was built, How fresh was the tooling? chamber reamers in particular, they do wear down, and they are sharpened to minimum standards before being replaced.
The bottom line is what die works best for any given rifle. If I fire this brass a few times and loose some that is fine by me.