I don't have enough experience building or playing a variety of basses to have an opinion.
But, I have talked to a very experienced builder (name withheld) and he says that with a neck through, the wood can get harmonics that are as long as the vibrating strings, setting up situations where you can have tones canceled out if the string vibration and body vibration are out of pahse. (I wonder then could you also have situations where certain tones are amplified if the string and body vibration are in phase?)
So his theory is that a bolt on neck creates two shorter sets of harmonics, one in the body and one (of a different length) in the neck, so that you avoid that cancelation of harmonics.
This may account for the reputaion that the bolt on seems to have for punch and the neck thru has for sustain.
The builder I know who prefers neck thru, prefers mainly from a stuctural strength perspective.
I am on my second build which is a bolton, my first was a neck thru. The neck trhu seemed like a much simpler way to build, because you don't have the issue of positioning and fastening the neck to the body. (I am building with no neck angle, that might make a difference in my perspective)