Not a custom rifle, but a buddy of mine bought a brand new Ruger No. 1 single shot in .25-06 that would do no better than three inch five shot groups at 100 yards with handloads or factory ammo. He sent it back to the factory after checking everything on the rifle (scope rings, good scope, good factory ammo, etc), and they said nothing was wrong with it and that it "met their accuracy standards". We loaded what seemed like a few thousand combinations, and the three inch groups came from rounds that were trimmed to uniform length, weight sorted, sorted for neck wall thickness, neck sized, all powder charges weighed and equal, and bullets seated with a floating sleeve straight line bullet seater. That rifle was the biggest tomato stake I had ever seen in 25 years of shooting centerfire rifles. He traded it in on a Remington 700 BDL in .25-06, put the same Leupold 3.5-10 that was on the Ruger on the Remington, and the same handloads went into 5/8 inch at 100 yards.
I had heard that Ruger No. 1s were finicky, but that rifle was the worst.
Just my .02,
LeonCarr