When I was more involved in the business, we sold a trainload of various factory rifles and very few failed to perform as desired. The more discerning customers had them glass bedded, had the trigger adjusted or tuned, and maybe had a different recoil pad installed. Sometimes the chamber might be altered by lengthening the throat. As a rule these rifles worked perfectly and did everything the owners asked of them.
I also built quite few custom rifles and soon learned that those worked best which deviated the least from standard specs. Unusally tight chambers accomplished nothing but diminished reliability. Closer tolerances were acceptable only where they had no effect. Things which might be of some benefit in a custom rifle would include such things as stock fit, balance, and over-all appearance.
I have seen custom rifles with rough chambers, crooked chambers, excessive headspace, triggers set too light, triggers set with insufficient over-travel, poor feeding, split stocks, and a host of other problems. Sometimes, some of these problems stemmed from the customer's cartridge choice orinsistence on a given trigger weight. Usually they came from the builder being too concerned with a given aspect of the build and neglecting overall function.
All of my present hunting rifles are sort of customs but most are pretty standard as far as specifications are concerned. Only one is a wildcat and none are built especially tight or to closer than normal tolerances except where there was some benefit to doing so. Ultimately, my only reason for using non-factory rifles is that I like to build them. GD