I don't think anybody would say that CNC operators aren't skilled.
It's not the point, either. If I wanted a cue churned out by a computer controlled machine, I'd just buy a production cue. I see no reason to pay a rather extreme premium if the cue is produced more or less the same way by an individual with smaller machines. Ok, you get someone selecting materials to MAYBE a higher standard (though Mezz for instance is doing this too), and maybe you can get a unique design (but maybe not, since the cues seem to be rather standardized and very few venture outside the norm).
I'd say buying custom, I'm paying for the cue being handmade and one of a kind or one of extremely few. The name of the guy programming a machine makes no difference to me. I'm rather more interested in the cue being handmade. That, to me, is what makes it special. If I didn't care for that at all, I could just as well order custom from a production/custom maker and skip the wait almost entirely, getting the cue within months or perhaps a year at most. It would still be somewhat unique.
I feel that you and others are confusing what a CNC mill can actually do. So first of all, using a CNC mill as part of the cue making process does not mean the cue is being churned out by a computer controlled machine. Let's just understand that and get it out of the way. Whether or not a cue is production or not, is defined by process and scale. Take McDermott for example; they have basically a factory with assembly line equipment designed for making cues so they can churn out as many quality cues as possible. This is different than from say Ned Morris or Chris Nitti or Bob Owen who are each individuals or part of a very small group that use similar equipment and manufacturing techniques to churn out a cue months at a time. It has nothing to do with whether CNC mill is involved or not.
Now, where CNC technology comes into play is the type of detail and precision you can put into the cue or anything for that matter with the assistance of computers. Now sure, you can have all your production equipment be controlled by computer programs and you just sit back and drink coffee and watch cues get made and that can be considered "production". However, that's not how most custom cue makers using CNC technology are doing it. Most are using it to create inlays that are not possible without a CNC mill, which actually makes a cue even more unique and "custom" that would have been otherwise. For example, Bob Owen uses CNC technology to assist in creating his cues. I challenge you to look and them and still honestly try to call them not custom.