They visited SpaceX, saw how they actually operated, and revised the estimated downward.
I'm not sure that's really fair for NASA to do. The question they were supposed to be answering was "how much would this cost NASA to do?". They can't just see a more efficient operation and then cheat their numbers down because without Space-X, NASA would never have had a reference to work off of. NASA doing it the NASA way would have been the larger figure, not NASA doing it the Space-X way.