re: What am I missing?
I certainly agree that not only below 200ft, but by the time you pass MDA/DA/DH you should be visual and looking for the runway (with approach lights in view) or looking at the runway itself, ideally the actual touchdown zone. If the touchdown zone is in view, the PAPI will be too, since it is longitudinally abeam the touchdown zone. The PAPI should be good reference while visual in extremely windy and limited visibility conditions. It was put there for a reason and designed for this very purpose.
We assume that trained and qualified pilots, ATPs especially, should be able to visually assess the aircraft's position for landing and complete the visual segment to a safe touchdown - or go around. Something in this particular approach event defeated that and the airplane touched down short of the runway.
Without placing blame on anyone, what is it in our system that we see such events? Was the airplane suitably stabilized on the approach? Was there sufficient visibility to conduct the localizer only approach and landing? Was something missing or optically illusional in the visual cues? Is more training and proficiency needed to actually fly the visual segment, and make the correct decision about landing or go-around?
If we cannot count on pilots to skillfully perform the visual segment - visually - then the safety basis for all but Cat III instrument approaches is faulty.