Fret size and bridge contact points. Larger bulbous frets would have more roundover edge for strings to contact than a thinner fret that would have comparatively less roundover and contact, same for the contact between the bridge and the string. This would affect sustain greatly, similar to the bearing edges on drums.
He's entertaining, but his 'science' is less than impressive, in my opinion:
If you listen to his strumming 11:34 to 12:10, the gooped up guitar is consistently less bright, and by quite a lot. I loaded the section into Logic, and split the bits into two tracks and synced up the strums. Here are the accumulated differences for all 2*5 strums in the analyzer (no prize for guessing which is which)
The way he is conducting the test, it is hard to tell if the difference is due to him consistently strumming differently, or if it is due to the changes he made to the guitar.
As is probably common knowledge, the overtones of a strummed string die out first, and towards the end of the sustain, it is mainy the fundamental that remains. Which is also why pickups with a lower and/or less tall resonance peak (think a fatter humbucker VS a Fender single coil for instance, or even the effect of a guitar cable with higher capacitance) will tend to give a perceived longer sustain, because the difference between the inital bright peak, and the end of the tone will seem less pronounced.
Because I think the different strums here are too inconsistent to qualify a deeper analysis of how quickly the top end of the signal is dropping off, or looking closer at the transient, I won't go deeper, but I'm disappointed that what could have been an end-all-discussions ends up botched by the experiment design.