My personal take - the shotgun barrel is fine - zeroing is not particularly critical here and it should be easy to pattern it on paper and see how it would shoot at shotgun ranges. The lower rifle barrel would be the one to be concerned about - changing calibers would be a problem as far as grouping is concerned. May be a better idea to have a rifle barrel on top so that the sights are on it and a change of barrel would bring a new set of sights which would be separately zeroed. This, of course, is the view of someone who was a boy when Moses wore shorts and who prefers open sights and not glass.

That said, would the lower rifle barrel reduce recoil as compared to putting it on top?