I guess the best way to explain it is when chrome flakes off it leaves a rough condition that will strip bullet jacket material. Once you start stripping jacket material from the first round you get a build up of copper that keeps on taking copper from follow on bullets.
The bullet has a separate core. Best accuracy requires that the core stay centered in the bullet jacket.
Once you start cutting grooves in the jacket which removes instead of engraving the bullet you will unbalance the bullet and regardless of what the rest of the barrel looks like you have already ruined the bullet before it clears the muzzle. You still have plenty of rifling to impart spin only problem is you are now spinning a couple hundred thou rpms with a unstable bullet because center of gravity has shifted off center.
I have pics of wear on barrels with far less wear (6000 rounds) and the dispersion was approximatley 8 feet at 600 meters where it should have been two feet max.
It is kind of like balancing a tire. I am sure you have had cars/trucks pass you on interstate and you see a wheel hopping so to speak. If the vehicle stops and you go up and examine the tire you won't actually see anything wrong with it. Placed on a balance machine and weights applied the same tire will appear to go to sleep rolling down the road.
I have seen bullets blow up going down range because of jacket failures. Other than having you continue to shoot your barrel until you decide it isn't accurate any longer and then cutting it as in picture and taking a look for yourself I really don't know what to say to convince you.
Just thought of a quick and dirty test you can perform to prove it yourself. Load up 50 rounds of your best load. First 10 rounds load them as normal. Next ten take a file and make a pass on one section of bullet. Next ten make a pass on two different sections of bullet say 45 degrees from that one. On the next 10 make another pass 90 degrees from the first one. On the last ten make a pass anywhere else on the bullet bearing surface you like. Make all your passes take off about .004" of metal. Do not cut all the way through the jacket.
Rifling is about .004" high depending on caliber. Shoot these in a new or perfect barrel and examine your groups. You might also weigh your bullets before and after jacket filing and record the amount of material you take off.
A cheaper test is to take a 22 target rifle with scope and shoot it for groups at say 100 yards. Determine what the ammo is capable of. Then start shaving off very small slivers of lead and shoot the same number of groups with that.
The term shot out has more to do with bullet distruction due to surface roughness causing copper build up than just removing rifling. On bolt rifles you can sometimes cut off threads on barrel, rethread and rechamber an inch down bore and the accuracy will come right back. All you have actually done is remove the roughness in front of the chamber because as you observe there is plenty of good rifling left in the bore.
Then again your definition of shot out and my definition may be worlds apart. My definition of shot out is the dispersion is unacceptable regardless of what the rest of the barrel looks like.
Unfortunately in the AR family we don't have the luxury of being able to set barrels back and you have three conditions in these barrels. New, in process of being shot out and shot out. The gov't standard of rejection is 7.2 inches at 100, the acceptance is 4.5" at 100.
A match shooter's rejection is 1 1/4" at 100 maybe 1.5" depending on his skill level.
It is well documented with photographs in various publications of bullet deformation causing enhanced dispersion. Basically you can deform the meplat and not get a very noticable effect on target but there are two things a bullet will not tolerate. Bearing surface deterioration (not to be confused with engraving from lands) and bullet base deformation.
Load say ten rounds of the load you use in the 50 round test above. On the base rim file one small spot off and load these and see what your results are.
And finally barrel manufacturers charge a enhanced price for lapping barrels. Lapped barrels have smoother surfaces, remove less jacket material which retains center of gravity and produces smaller group sizes.
All I can tell you is if you keep shooting your rifle barrel the groups will at some point start to get bigger and will keep on getting bigger. It is your decision when you decide that enough is enough and you want smaller groups again. If it gets bad enough you will see deterioration in bullet stability in as close as 25 yards. It will take you awhile but sit down and shoot a 3X5 parallel card for ten shots at a dot on the card. At 5000 rounds do it again and 10,000 do it again. At some point you will see bullet holes become elongated (egg shaped). Your group sizes will get larger even at 25 yards.
You just have to decide what is acceptable for you.