I drive with the tailgate window down all the time because my dog likes to hang his head out the back. I got the exhaust smell until I cut the exhaust pipe right after the bend that goes over the axle. You can either do that or have tail pipe re-routed to exit on the side.
I can smell exhaust when I drive with it rolled down. I can leave it a little cracked, but not much. It's not so bad when I leave all the other windows up. Only time I drive with it open is to evacuate the hot air after its been sitting in the sun. After the temp equalizes with outside air I close it up and turn on AC. That was one of the two selling points when I chose T4R over Xterra.
One of the main buying points to me was the ability to roll down the rear window(you don't find this option much) but when the chance/need comes to re-rout the exhaust to the side I will.