“I see a few possibilities”
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Nothing wrong with speculating, but I do not see any of those as a cause. I am not a commercial pilot. I had only a Beach Bonanza, so I comment only as a SEL pilot.
I understand that he had excellent VFR conditions, so the altimeter and your other concerns would be of little consequence, unless he was practicing under a hood...not at all likely. He should have been able to safely land with no instruments at all.
I do not know the runway length, but touching down at the threshold would be quite strange, I would think.
All I can think of is that he was very distracted by something, or a mechanical failure.
With no glideslope?