I believe there was a factory upgrade option for full-size spare, or else I just lucked out with the car I bought. It has a foam structure around the wheel well that raises the cargo floor up to sit flat over the full-size wheel, and the floor mat also has a rolled lip at the rear to neatly meet the tailgate opening (and punk you by making your shopping bags roll out if you leave them too far toward the back).
Unfortunately with the 18" wheel not nestling all the way down, mine now also has a (slight) hump, which really bugs me.
I'll let you know if I decide to get rid of the 16" spare, there's a chance I might go back to it if I can't make this one satisfactory...