It's similar, but not identical to the models without the 3rd row. I remember a thread where someone was researching putting OEM 3rd row seats in his non-3rd row model and there were significant floor mounting differences.
The few details I remember offhand:
The 60/40 split on the 2nd row seating is opposite on the 3rd row vehicles.
Also, the 2nd row seating reclines on 3rd row vehicles.
There is no slide out shelf in the cargo area.
The 3rd row seats are mostly out of the way if not in use and flip up close to the rear side windows. They can be completely removed from the vehicle easily enough as well.
IMO, if you are looking for a good 4runner and come across one with 3rd row seats, there's no reason to avoid it. They are generally rare and there are often folks scouring the classifieds for these models, however.
I've debated selling mine but then realize I can't get a 5th gen with a V8