I would still provide the 3" cover. Typically, we try to place the steel as high up as we can - 3/4" cover on the top, say - to assist in keeping cracks as closed as possible on the top surface (which is the focus of the steel in the first place).
In an expansive clay situation, your 5" slab reinforcing is not going to really help in adding stiffness to your slab to help in structural behavior during shrink/heave cycles, especially if its in the middle. I would still want the rebar in the top to keep cracks closed on the surface, knowing I've got larger crack widths developing in the lower regions.
If I want to stiffen the slab to minimize localized heave, I would use a stiffened slab made up of monolithic concrete ribs, or beams, in a grid pattern under the slab.