I've never had a problem with "out of spec" throats either; all were within factory "specs". Just never had a Blackhawk where every throat was the same on any given gun, except the 41s.. There was always some variation, usually 1 or 2 different chambers. Every 41 I've owned (9 that I can recall) has had consistent .411" throats.
"Not sure I understand the drill fully. Do I want cylinder chamber sizes to be greater than barrel throat size, but not by a great amount, and I want the bullet size a small amount larger than the largest cylinder chamber?"
Think of your gun as a funnel. Largest at the throat and smallest at the barrel crown. You should be aiming for consistency of your chamber throats. Theoretically, at least, consistency here gives you a better chance of accuracy, but every gun is different. And there are so many other contributing factors, it's hard to nail anything down without actual shooting. Bore diameter, groove diameter, internal barrel finish quality, bore constriction or not, boolit size and fit, boolit hardness, chamber alignment, etc.