When luthiers and guitar players say that neck-thrus have more sustain than any other neck joint, they don't mean any neck-thru... it's likely that a Krappy custom neck-thru will have less sustain than an Universe.
And I strongly disagree that the greater sustain in a neck-thru is a myth.
It's a plain physical fact:
The sound we listen to is the result of mechanical waves propagation, which doesn't occur without the presence of a material mean.
All particles in a body hold a certain amount of energy, which allows the matter to keep it's properties.
All particles in a body have a certain region upon which their positions may vary. The stronger the bond a particle has toward another one, the more smaller that region will be, thus yielding their geometry (display in space) to be more rigid.
Waves are basically energy travelling across space. When a wave hits a body, part of it's energy can be converted into work such as temperature raise or mechanical vibration.
Now, this is a generic wood particle electron in a normal day:
(normal oscilation range)
Then, one day Hoshino Gakki Inc. chops it's tree down and builds a LACS Xiphos for Muhammed.
And the particle goes like (with an ENGL Powerball):
(wider, energized oscilation range)
What happens is that when that particle was struck by the sound wave, part of it's energy was retained by the particle and raised it's energy level causing it to shake harder(!).
Tip: The higher the density of a wood is, the better it's sound wave transmission is, because it's particles are strongerly bound, causing very small wave attenuation or absorption.
In a neck-thru body, the continuous link of many wood particles provide a true free lane for the sound waves that pass all the way through it up to the pickups and hardware.
In a bolt-on, the non-natural bond of bolts introduce an abrupt mean shift for the waves, causing some of the sound waves to be absorved by that separation surface and some to be reflected back into the neck.
Of course we should take the refraction phenomena in account, but that would only give the neck-thru some extra points.