I guess I have a bit of a different take on this-having spent most of my life working with metal(auto work, engine assembly and machine work), and the last 20 years working with wood(wine cellars, finish carpentry,etc). One of the really great characteristics of wood as a material is the individual character and personality of each piece- as contrasted with a material such as metal, where the beauty is the absolute consistency of it from piece to piece. Seems to me that the most important thing here is that the operator of a CNC machine has to respect this, and work with the "personality" of each individual body blank in setting up the cut. I have a couple of handmade instruments, and some CNC-cut ones, too. All of them offer stellar quality, and play really well. The difference for me with my handmade instruments is that, when I look at or play them, I'm aware that a highly creative,skilled and experienced luthier made hundreds of decisions about how to build the instrument, and then spent a lot of hours creating the instrument by hand.
So to me, two types of instruments are different, even though they all play equally well. The handmade basses are more meaningful to me, because they more reflect the personality and vision of the builder-but my main player is a CNC-cut bass. Go figure.