Dave, I agree a set-neck will not sound like a neck-through, but there's a greater similarity between SN and NT than between SN and BO. To put it bluntly, BO is basically a body with a neck nailed onto it while SN is a body married to a neck by a dovetail joint.
 
I guess the effect of the joint would be evident when you could A/B an all maple SN to an all maple NT with similar electronics and strings.