Bolt-ons have much more harmonic content to the notes (snap, shimmer, spank, pick your adjective)
Neck Thrus emphasize the fundamental content of the note (deeper resonance, thicker growlier punchier tone)
Set Neck is in between them
It has all to do with the mechanics of the neck joint (or lack thereof - there is no neck joint on a neck thru), meaning how much string energy is "lost" between the neck plank and body. Bolt-on's don't transfer low end frequencies as well, thus their emphasis on the harmonic end of the spectrum. However, the human ear and brain sort of "fills in" and extrapolates the missing low end similar to how the tiny speaker works on a telephone. You hear a male voice sound normal when listening but that tiny phone speaker is not really capable of reproducing the lower frequencies of that person. Hope you enjoyed today's nerd out session.