Howdy Again
You are absolutely correct. Modern S&W revolvers have a groove running the length of the extractor rod and a square 'key' raised on the ID of the cylinder hole that rides in the groove. I have no idea how they milled a square key inside a hole, perhaps it was broached, but S&W Hand Ejectors had that for many, many years. Just looked at a MIM era Model 617 and it does not have the groove, the shaft has a flat on it. There is a corresponding flat inside the cylinder 'hole' that keys off the flat on the shaft. Again, I don't know how they get a flat inside a hole, perhaps broached, perhaps Wire EDM. Clearly it is less expensive to do it this way than put that tiny square ridge inside the hole the way they used to do it,
Here is the arrangement on an original Schofield. The groove has angled edges. There is a very small, triangular nub on the inside of the cylinder hole that rides in the groove. Again, not sure how they raised the triangular nub inside the hole. I am assuming it runs all the way through the hole. No, I am not going to take the cylinder apart to find out. Clearly Uberti took a small production shortcut making a hexagonal shaft. Not sure how they made a hexagonal hole, perhaps they Wire EDMed it. Nothing wrong with a minor engineering change to make it possible to make an affordable replica.
Regarding Schofield rims overlapping in your cylinder, you might be pleasantly surprised. Starline 45 Schofield rims are running .518 - .519 in diameter. Yes, I measured some.
Let's take the worst case scenario. A rim .519 in diameter is .010 larger than your .509 diameter Winchester 45 Colt rim. That means the .0165 worst case scenario between cases on your cylinder would be reduced to .0065 between rims. Did I get my math correct? Plus, don't forget there is always a tiny amount of slop.
Many years ago I had my favorite gunsmith open up the counterbores on a Remington 1858 45 Colt conversion cylinder slightly. As built the counterbores would not accept a 45 Schofield rim. Before he opened up the counterbores he did the math, and determined there was not enough distance between chambers on this cylinder to allow the Schofield rims to seat next to each other without over lapping. He went ahead and opened up the counterbores anyway. It turns out, there was just enough slop between the OD of the cartridges and the ID of the chambers that the Schofield cases fit in very nicely, despite what the math said. A teeny bit of slop can sometimes go a long way.
Tell you what I'll do. You send me a private message with your name and address, and I will send you 6 pieces of 45 Schofield brass and you can find out for yourself.
Gotta warn you, they won't be virgin brass, they have been fired a bunch of times with Black Powder so they are stained, but they will serve to see if a teeny bit of slop will allow you to chamber 45 Schofield brass.