Can't say any difference in sound I've heard is attributable to that and not pickups, body wood, neck wood, fretboard wood, fret size/material, string gauge/material, electronics, pickup style, pickup brand, pickup height, body finish, neck finish, string trees, lack of string trees, day of the week, or any combination of these.
Excellent point. It's just one of many variables. In order to determine a difference, you would have to build multiple basses with identical specs EXCEPT bolt on vs. neck thru. That's why I tend to listen to guys who have that kind of experience. From the FBass website FAQ section:
Does Neck-Through construction sound better than Bolt-On?
“Better” is subjective to the player.
We actually find that a wider range of players prefer Bolt-On. It has a quicker attack & an overall more lively tone, is more responsive to playing dynamics, doesn’t render the entire bass worthless if the neck is damaged beyond repair, and it’s standard to boot. The neck-through construction has always and will always be an option for those who want a little more compression and sustain. It’s a positively beautiful thing in the upper register.