There's no doubt that automated manufacturing is the best way to repeat a design millions of times in a row. But if there is a design flaw, all of them will have it.

However, the natural partner of CAM (Computer Aided Manfacturing) is CAD (Computer Aided Design)... and it is the CAD that has improved the designs of complex items like musical instruments.

In much the same way as virtual instruments can be modelled in plugins (because mathematical traits of the sounds they make are known) design engineers can experiment with all the attributes of an instrument while they build the CAD model from which the instrument will later be machined.

Effects of fret spacing, wood type, neck length, wood mass and density can all be played with while the CAD model is still bits and bytes. A small time luthier would have to make real instruments to test his theories, and the time involved would dramatically reduce the number of possibilities he could test in his entire career.

This is not to say that every luthier with a CNC router uses all the power of CAD to design his instrument. But I bet the big boys do.

For this reason I think production line instruments provide the best "bang for the buck", because the design is more likely to be continuously tweaked from a mathematical model and then those tweaks are reproduced accurately in every subsequent instrument.