The article OP linked to poses the problem very nicely. And this thread picks up on most of the issues. Not being a theologian I can't really talk to the soul of an object, hand made or otherwise. And, though I'm accused of being a romantic occasionally, my romantic tendencies incline toward women and ideas more than guns and dogs.
So, personally my taste runs towards custom made rather than hand made, and CNC tooling for the innards and hand checkering/engraving on the outside. That's just me and your mileage may vary.
As for why we haven't seen any cost reduction from the adoption of CNC production, I suspect two factors are in play--a return on the brand equity that owners of makers such as Purdy's and H&H expect (European luxury goods conglomerates in both cases) and the small production volumes over which tooling costs must be amortized.
Before the Spanish started having their problems, the perception that a 'Spanish best' was 90% of a London gun at 10% of the price was common. Most of that was brand premium. But--people wear bespoke suits and walk on hand knotted rugs and shoot London bests for all kinds of reasons, and clothing their nakedness, keeping the mud off their boots and putting a bird in the pot have very little to do with it.
Yes. A lot well said here, in relatively few words.
Jay