In many cases it may be the factory methodology as much as the tooling dimensions which result in larger chambers. In other words, they may not take the care in alignment that a gunsmith must. Remington, for instance, finishes their chambers with a reamer which is run through the bore and clamped in a collet. The reamer turns while the barreled action is held in a vee block clamp. The bolt is closed on the base of the reamer and when the bolt closes, the chamber is done. If the bore is curved (common), side pressure may cause the reamer to cut a chamber which is misaligned or over sized.
Occasionally, the reamed finish is so poor that excessive polishing is required to get the rifle to function at all. In many cases though, the factory rifle is simply not built to SAAMI specs at all. This is the only explanation for the wide variation in throat length, diameter. or configuration.
When it omes to set-up errors, it is not only the factories which make them. I have seen a lot of custom chambers which were over sized, eccentric, or over polished. One gunsmith I know was complaining that his reamer was cutting over sized chambers and he was going to send it back. The reamer measured OK and it turned out the problem was in his lathe set-up in combination with poor technique.
I am not immune. I once had offset my tailstock slightly (about ten thou)to taper a shaft and din't re-align it right away. I forgot all about it and was chambering a 30/06 barrel a couple days later. The reamer didn't seem to be cutting all that well and when I stopped to check chamber depth, it was obvious the chamber was oversized at the base. I realized immediately what I had done but it was too late and I had to buy a nother barrel for that customer. I still have that barrel under the bench as a reminder.
Special reamers, as ordered by gunsmiths, are usually special only in throat dimension although some will order reamers which are very tight to minimize brass expansion at the web or at the neck. In general such alterations in SAAMI specs are important only in the mind of the guy doing the ordering and most will find the SAAMI minimum will work just fine.
I think the intended use of the rifle is the one factor which may influence chamber dimensions. If one is making a custom hunting rifle, that rifle is supposed to work better than the run-of -the-mill factory offering. If the chamber is too tight and the rifle is fussy to use and load for, it's not better.
On the other hand, if a rifle is built as a precision varminter or amatch rifle, the gunsmith may vary chamber dimensions in an attempt to improve performance at the target. A benchrest rifle is expected to require considerable brass preparation, for instance.
Often times, a customer may want to load a given bullet to a specific overall length. In this case a throat may have to be cut longer than standard. The gunsmith will either order a reamer with a special throat or he may elect to cut the throat with a separate throating reamer.
Although I am convinced that reamer dimensions have little effect on rifle performance at the target, I have been as OCD as anyone at times when agonizing over the spec sheet so I understand how it can go.
To sum up, it is true that "tight custom chambers" exist but they are not always a good thing. Concentricity and alignment means a lot more than dimensional variation. GD