I don't know about tone, but in my experience the neck through is more stable.
I have a '94 Carvin and a '16 4003 s. both neck though and I do not remember ever touching the truss rod on either. If a gun was held to my head, I couldn't even be sure if either had them.
My Fender Jazz and Ibby SR650 are both bolt on and I have had to adjust the truss rod a few times on each.
The Carvin and RIC also seem to hold tune better as well. I have to tweek the bolt on's every time I play them. The neck through seem to be once a week unless I bump a tuner.
Of course I can be full of crap too, this is just my experience