I took mine on a trip to Africa and noticed the same thing.
My Handi came as a 3 barreled package with a 12 ga barrel, 243 with scope, and a .50 cal muzzle loader. Mine has a monte carlo stock, which I think affects the sight picture and makes the shotgun barrel aim high. I think the MC stock is OK for the .243 with scope, but too high for proper alignment for the shotgun barrel bead.
I've been thinking about modifying the stock to lower my eye alignment, or else installing a Red Dot scope which will sit higher on the barrel and may offer more accurate sight alignment.