I have not toured every prefit barrel factory, nor have I talked to people that claim to have. I used to shoot barrels by a particular prefit company (not Proof). My gunsmith also happened to be sponsored by them and toured the factory. They did not indicate the bore to the accuracy a top smith will or by the same method. Once having had this discussion, I bought a testing borescope and cleaned and examined the throat in all of said prefits. The ones that shot good and weren't picky had concentric looking throats. The ones that were very picky and didn't shoot as well has VISIBLY crooked throats where the start of each land was offset. These barrels are 1/2 the price of a prefit done to my specs by my gunsmith, so I continued to use them for high volume stuff where good enough accuracy was acceptable.
The barrels I had chambered and threaded by my gunsmith (even when using blanks from the above mfg) have all been very easy to load for. They shoot everything that isn't overdressed into 3/8 groups for 5 shots at 100 yards. (since most still use that as the standard comparison metric). All the chambers look straight. He indicates the bore with a long stem indicator until in run 0, so the bore should be as concentric as the accuracy of his indicator unless something causes the reamer to run wonky. I have now had 7 barrels from him and all have shot great with ZERO load development. You can literally see the difference in components quality when shooting his barrels. Good lots of Berger and it shoots like a benchrest gun. Groups open up with great Hornady/average Berger lots, average Hornady lots, and bad Hornady lots. So far, I haven't found a lot of Bergers that shoot bad.
It is possible that proof indicates the bore of every barrel with a long stem indicator. The pride in outcome situation still applies. I have heard a lot of good things about Proof prefits from average skill level match shooters. I also know a couple guys that can put 5 bullets in a single hole at 100 yards that refuse to even use their barrel blanks due to bad experiences (in Proof's defense, I don't think they ever used CS, just went back to what was working before).
I have had discussions with Josh at PVA online about indicating. He said it is something they refuse to compromise on, and he is trying to figure out a way to be price competitive with the prefit companies like Criterion, and still put out a chamber that is indicated to .0001" so it will shoot to his standards. He said that was the time bottleneck that prevented him from being price competitive with them.
Based on that, I assume, if the price for the prefit is much cheaper than a PVA, they probably aren't being indicated for concentricity in the same manner.
There are always compromises. Many one man shops have long lead times and are bad at giving accurate lead times. If you look around, you will find a few shops that are good at giving accurate lead times and do exceptional work.