This is my basic process:
I use a tap to clean out the breech end of the barrel (there is usually a burr or whatever at the bottom) - I use a plug tap for that which doesn't exactly leave a "squared" shoulder - there is a tiny taper - but it is minimal.
I then measure the depth with the caliper.
I run the plug through a die to clean up the threads and try a quick fit (with anti-seize on the plug) to make sure it's not loose etc - want a tight fit or I get another plug (never had to yet).
Clean up the plug and measure the journal, mark it leaving a few thou extra - mark it with a magic marker and then wind it back into the die.
I use the die as a guide and file the plug down to my mark (almost - I leave the mark "just recessed" into the die).
The top of the die leaves me a nice flat surface to file the plug to and it's "hard enough" that the file skips over the die when I get down there.
I then use a magic marker to (paint) the plug face and screw her in until "snug".
Back it out, file anywhere (a couple of swipes) where the marker has been smudged, paint it again and repeat.
I keep doing that until I am about 1/3 of a flat from where I want to "finish".
When I get there using "some hand pressure" to make it snug, I call that good and give it a quick torque to get it lined up where I want it.
I do pull the plugs and if you put a straight edge on them, the face is never "perfectly flat", there is a tiny taper.
That's my system.
If the breech is threaded "deeper" than the plug journal I usually grind it down a bit (bench grinder/jig) before I work on it with the file.
If the barrel needs work, I do that first - shooting for .510" thread depth which gives me a little "wiggle room" should it need some file work to square it up.
So the barrel gets "squared", the breech plug face does "not" (at least not exactly).
Works for me - others may differ...