Well I'm trying to figure out a way to check things.... If you have a rod of any sort that is smaller in diameter than the bore- can you slide it down the bore and test the sides of the chambers. Let's say, looking down the barrel from the muzzle end, when you slide the rod down the right side of the bore it hangs up on the chamber wall but it passes ok when you run the rod down the top, bottom, and left of the bore. I'm just thinking here and hopefully others will contribute, but maybe the cut that the bolt passes through is off. If the bolt locks up ok, the shape of the bolt is fine, you need to move it a little to one side. See if there is a manufacturing burr on the opening for the bolt.
The burr might be the most logical since the manufacturing process for the chamber locations, etc ought to be the same from gun to gun. The location of the opening in the frame for the bolt ought to be the same from gun to gun. Some sort of burr could have moved the bolt to one side, causing the cylinder to turn a little far or short and cause the slight misalignment.
You might have to remove a little material on one side of the cut for the bolt. If that creates too much of an opening- then peen a little on the opposite side- but as I said, if you are still in the buying stage of things- unless the price is very low- I'd just look for another gun that lines up ok.
Since the lockwork is the same as any Colt Revolver (Cowboy 1873 Peacemaker) Maybe you could search the net for a gunsmith that works on Colts and ask him about the problem.