I'm not one who can speak from experience about jug choking a modern SXS, but I do have a muzzleloading New England Fowler with a 51 inch barrel jug choked thirty thousandts. It is deadly on turkeys at 40-42 yards which is looong for a muzzleloader. Personally I can't see how it would make any difference wheather the piece was a shell gun or a muzzleloader! Why would the ignition system have any effect on the shot column moving down a barrel?
One thing I can say speaking from experience in shooting a flintlock SXS that should hold for a hammergun also....if you are going to have one barrel choked and one cyl bore, you will find it much easier to have the right barrel choked and the left cyl bore. The reason is that unless you back both hammers before you take a shot, it is much easier and quicker to reach up and back the right hammer for the second shot than it is to reach over the right hammer to back the left one. A very good friend suggested this to me when I recently had another set of barrels made for my flintlock, and he was totally right!