They are taller due to the fully boxed frame needing to be taller for strength. You also cannot set stuff "in" a fully boxed frame like you can on a C channel frame which means you have to place everything on top so to speak. One of the draw backs of a fully boxed frame along with how much harder it is to add a utility bed.
As far as wheels go, I don't think you can go smaller than a 17 inch wheel on these trucks due to the brake size. However, a small diameter wheel on the same diameter of tire as before will do nothing for your ride height. You will have to reduce overall tire diameter if you want to lower truck height which you can do(to a point) without reducing wheels size.