my guess: to relieve suction in mudholes. you get a big, flat plate under a vehicle, drop it into a mudhole and get stuck, and it's gonna be twice as hard to get out because of the suction.
edit: my stock skidplate (or at least the skidplate that was on the tracker when i bought it) wouldn't fit back on because of the differential drop. one of my future projects is to fab up some blocks so i can put the skidplate back on.