Beam too close to ceiling for fixture
Looks like the small diameter nipple screws into the shorter, larger diameter 'nipple', and the second nut is acting as a locknut. Once the locknut is loosened, the inner nipple ought to unscrew with finger pressure from inside the larger, shorter threaded 'nipple'.

Once the locknut is off, you might be able to screw in the nipple deeper. Or you could cut it off without risking damaging the wires, or you could replace it with a shorter nipple (available at local hardware store, Home Depot, Lowes, etc)