I retired 6 years ago and so my info is not current but when I retired some of the Secret Squirrel types were using .40 S&W hand and sub guns. Both Federal and Winchester load pistol caliber ammo for the DOD. It is all NATO spec with crimped primers. In fact, for some years before my retirement the DOD was not producing it's own ball pistol ammo. I was all coming from the civilian makers and I haven't heard of any change.
They have also loaded very high pressure "submachinegun only" and subsonic stuff for military and police applications, too.
I'd try a primer pocket swaging tool and see how that works. The RCBS one is inexpensive, uses your existing press and works well. The Dillon one is a bench mounted tool and is the hands down winner as a high production tool. Pick your price point....
Hope this helps.
Lance