The main difference is in comfort. The 4" barrel requires a longer holster. The muzzle are presses against your back pocket, which is rounded on the inside. This creates a bit of tension thst you feel as you move around. You can see this printing sometimes. The 3" gun, WITH A HOLSTER MADE FOR IT, will relieve some of that tension. If you carry the 686 3" in a holster made for a 4", you will either feel a slight difference as the leather is mashed down over time or no change ever if you use kydex.

I also think the 4" is easier to shoot. I noticed a dramatic difeerence in performance when moving to a 3" gun from a 5" gun.