The only way that a bolt on neck will transfer vibrations better is if you hit some weird resonances and get two different parts and types of wood to produce louder output and more sustain... which is unlikely to work for all notes, it could work for a note or two, in which case you have a serious problem. For purposes of output and sustain, NT is unmatched due to simple physics. Set in neck is losing some sustain and loudness (as well as getting damped) by the glue, so NT still wins there. But if the real debate is 'how much is there a perceivable difference and what do we really need' then I'd say all three types of neck-body relationships are perfectly fine. It's also important to mention that technically, set in and bolt on necks produce more attack. There's no more attack per se, it's just that there's more damping which makes the attack less prone to getting lost in transfer while the body of the note gets lost a bit. To picture this, you have to realize that the whole neck is vibrating. The more it vibrates the more matter around it it will move along with it, and so it will affect the body more. As it starts vibrating less, it is less likely to affect the body a lot because of the distance between neck and body (what we see as two objects touching one another could be microns away, which is huge for this application). But still, some people simply don't like the way NT design damps (or that is, doesn't) the note. Really trained ears like BO system more because it damps notes more and in a way produces more attack. Another thing people forget is that if you have neck through design guitar has to sound different because it has more of the neck wood in the total amount of wood on guitar, and it's in the most critical place, meaning that the difference you're hearing is more so the fact that there's more neck wood (maple, bubinga, mahoganny, etc) than what's used for the body (or in this case, the wings). Obviously an alder bass with a bolt on neck will sound drastically different to a neck through bass with a maple/mahoganny laminated neck with alder wings. This is one of reasons why it's impossible to a/b this correctly.
TL;DR:
Going down to micron levels, neck will always be farther from the body on BO and set neck basses, meaning the smaller the amplitude of the vibration is, the less will transfer, which means that NT basses have the best way of getting loudness, sustain and even dynamics. But still, that might not be what you're after, some people have even put foam under strings to dampen them... So if you have really good ears to tell, you might not like NT system because it doesn't dampen string vibrations enough.