The way I understand it, the ammonia neutralizes the corrosive salts from the berdan primers used in milsurp ammo... Though with 54R, pretty much everything is going to be at least mildly corrosive.
I actually bought some copper solvent called Sweet's 7.62 on the reccomendation of a milsurp shooter/collecter friend of mine. Don't use it with a bronze brush, though.
The Sweet's does include ammonia, but afterwords, I'm running Hoppes solvent through the barrel since that stuff is also corrosion inhibitor, and I don't feel comfortable leaving stuff that eats copper in my barrel for very long.
Since I think I revealed barrel that hasn't seen air in 60 or so years, I dried all the solvent out of my barrel and gave it a good coat of Rem Oil. I figured a bit of Teflon couldn't hurt, and some oil might help break up what's in the barrel. I'll be hitting the cleaning supplies again this weekend, but I'll need a new cleaning kit, since the Mosin's issue kit didn't come with a brush (only part I didn't get) and I broke my Hoppes cleaning rod pushing a patch through the barrel (it came partway unscrewed) so I finished cleaning with the issue kit.
I'll get her clean, probably this weekend. After I cash my paycheck today, I'm stopping and getting a new Hoppes cleaning rod, and I'll look for a bronze brush (I have a brush, but it's nylon, talk about worthless.)
Oh, and patches. Must not forget patches. I actually ran out and wound up saving a couple for the final swab-out, and used chunks of paper towel for much of the cleaning.