I asked myself the same question when I first encountered a custom knife maker that used a CNC machine, during my initial fascination and introduction in the custom knife world. My initial reaction was one of outrage and blasphemy...calling themselves custom knife makers. But the more I thought about it the more I realized it's merely a matter of personal perspective. Personally, I don't consider CNC made knives to be custom...when you compare them to knives that aren't made with a CNC machine.
I imagine it has to do with the fact that I came into knife making with preconceived notions and ideals of what constitutes a custom made knife. I'm a video game artist by trade, so creating something by hand, for me, gives the object soul that can be seen and experienced through the imperfections...or lack thereof. Once something is created by the use of software, no matter how much skill and dedication it requires, the soul that is transfered to that object is somewhat diminished or lost.
Just my thoughts on the subject.