Mattia, you are right on the money. Cnc is not a "quick draw it on the computer and push the magic botton kinda thing". I would probably be time and money ahead if I had just learned to do it by hand. And so much of what makes a great guitar, things like fretwork and setup, can't be done by a machine.
These are the aspects of my first guitar that intimidate me.
I think what gets most of the cnc guys riled up is the attitude that your cnc built guitar is not as good because the machine did all the work. I've run into alot of this kind of thinking in different places on the net. It's easy to assume anyone who raises a questioning opinion on using cnc comes from this school of thought. Mattia though, you clearly know what is involved, and your opinions are right on the money.