Quattro, it has all got to do with the design of the guitar. How do you want it to look,sound, play etc. There is no bonus of one over the other, some people like a set neck because generally you get better fret access and the guitar generally has better sustain, others prefer the percussive attack of a bolt-on joint. Leo made a bolt-on style joint on fenders so it could be replaced if the neck got damaged.
The point im making is, look at your design of the guitar your building and work out what fits best. If you glue a bolt-on style in and shape the joint for better fret access what will it do to the strength of the joint? It still has to support the pressure of string pull... Or, should you change the design of the neck joint so when you glue it and shape it, it will have the required strength.
Doug pretty much summed it up in the last line of his post.
If you give us some insight in your design we may be able to guide you in the right direction.
Chad