I don't think that bolt on vs. neck affects tone much (bolt on is superior IMHO) but neck through guitars do seem to make a slight difference.
I am going to disagree with you on that one. Talking guitars only. Bass is a different thing.
Neck thru guitars do, IMHO, feel and sound different, better in my opinion. And here is why, again just my opinion. The multi piece laminated necks are incredibly stiff. And because of the neck thru approach, the neck is longer than a bolt on or set neck. This longer piece of laminated wood, due it's longer length, has a lower resonant frequency. Low enough so it does not effect the sound. Low enough so that normal string vibration does not get the neck vibrating at resonant frequency.
I am currently playing a set neck and the neck vibrates like crazy when you play it. This means that energy is being absorbed by the neck and removing the energy from the string.
There definitely something different, better IMHO, about a neck thru. Recently played a Wolf neck thru that was very, very nice. Neck was stiff as can be. The entire Alembic/Irwin legacy is based on this approach, the must be a reason. (admittingly, Irwin deviated with Tiger, it is a set neck.)