I agree with you and certainly wont argue with John but ive seen it both ways. Ive owned linebored guns with match barrels that shot fantastic and ive had them that shot average. Ive had out of the box rugers that have shot great and ones that shot average and even a couple that did poor. One 45 vaquero I had that was so loose after shooting BIG loads for years that it sounded like a rattle when you shook it. That gun shot fantastic but it bothered me that it was getting so loose so I sent it to a very reputable gunsmith to put a new match barrel on and fit it up tighter. It wasn't linebored it was fitted up like John does them. He doesn't linebore (at least didn't use to) The gun came back and went from an exceptional shooter to just an average shooter. So there can be more at work here then just fitting. John himself said that he can build 5 guns with the same barrels and same fitting and 4 will be exceptional and one might not be and he himself doesn't even have the answers to why. Point of this is that just because a sixgun is fit up tight and precise its no real guarantee its going to be a one hole gun at 50 yards. Chances are it will at least be a decent shooting gun but theres no guarantees.
I had two guns built at the same time by a reputable gunsmith. Both on old model rugers. One a 41 mag that was just punched out to 41 and had a new 41 cal barrel on put on it. The other a 44 special that was a full custom linebored guns. The 41 hands down outshoots the 44 special. Ill also add that the two most accurate handguns ive ever shot (neither mine) were a super redhawk 44 mag and a 44 mag Blackhawk hunter. Both owned by different people and both would shoot groups at a 100 yards that a guy with a bolt rifle would be proud of. Ive got right now 8 custom sixguns and five guns in the safe and wouldn't put a single one up against those two sixguns.