I should clarify my comment about bolt-on and set-neck being functionally equivalent. As opposed to a through-body, both set-neck and bolt-on are different pieces of wood under nut and tailpiece and I think that dominates the tonal effect.
But actually building a set-neck instrument is much, much harder than a bolt-on. Not only does it require greater precision in the joinery, but you have to design the overall layout of the instrument to accomodate the set-neck as well, in particular, the fact that the body-to-neck angle is fixed, just as a through-body is. From a practical standpoint, this means special care must be taken so that the bridge height is right. On a bolt-on, if a particular bridge is too tall or too short, you can shim the neck to change the neck angle. With set-neck or through-body, you have to elevate or inlay the bridge into the body.
The big difference between set-neck and bolt-on is that the bolt-on will be more likely to require a heel that might interfere with access to the higher frets. Many clever designs try to work around this, but it's pretty hard to design a functional bolt-on that yields clear access to the 24th fret like a through-body Alembic. The set-neck will give the designer a lot more flexibility to shape the heel and can conceivably offer more access up there. For some people that matters, for most, I would guess it's not a big deal.
You certainly can build premium bolt-on basses. MTD is the obvious example. It's pretty terrifying to consider a $4000 bolt-on bass, but Mike Tobias didn't pick that design so he could crank out basses! There aren't very many set-neck basses - a lot of Gibsons over the years and Zon come to mind, and I have one of the original PRS basses that is set neck as well.
I think that the Bass Player-type mags seem to have really overemphasized the neck pocket and neck joint tightness in their instrument reviews these days. Aligning the bolt pattern and neck properly are critical, but in my mind, there's nothing wrong if there's a small gap between the pieces or a shim in the pocket. Tighten those 3, 4, 5, or 6 screws and the joint will be appropriately tight.
I also think that a less rigid sustain block alternative would be a very interesting experiment. I tried chopping up some polyurethane skateboard wheels which I think would be a very interesting material, but was unable to make anything stable enough to play. I think this would have needed to be done by casting a polyurethane block with the appropriate threaded inserts in it. An easier experiment would probably be having a like-sized block cut from some other material (aluminum?) although this probably wouldn't be as interesting as a more elastic material.
