I've never seen a barrel marked "3 INCH ONLY"; but, that doesn't mean one doesn't exist. Many folks get confused when they buy new Remington replacement barrels, for older guns, since they stopped making 2-3/4" chambered barrels and have 3" chambers in the replacement barrels for 2-3/4" actions.
A shogun isn't like a pistol where there's a ledge in the chamber. The shotgun's chamber transitions to the bore diameter with a tapered section known as the forcing cone. As long as the end of the opened shell doesn't enter the forcing cone, you're okay.
What barrel (and for what gun) is marked for 3" only and how exactly is the warning worded?