Actually, the general area that Artas extracts from is completely controlled by the Dr. (while of course the specific follicles to pluck are chosen by Artas. Here is my understanding of how it worked, and I apologize in advance to any techies out there that know more details than me, but below is my experience and my understanding.
The 'Template' I described earlier, to my understanding was attached to some area on the back of my head. It's almost like a metal surgical drape to speak of, and exposed a small area on the back of my head where the Artas punch would work. I think they referred to it as a 'grid' as they were working. Once Artas was done working that 'grid' they would move the template to another part of the back of my head where Artas would again extract from. Also from what I understand, the Dr., also controls things like the depth of the punch.
The doctor I went to did tell me quite a bit about who is a good candidate for Artas and who is not. In my case, I have fairly dark hair with only a small bit of grey that was of a certain density on the back of my head, and so according to the Dr. that made me a good candidate.
I read the post you were talking about with the 5000 graft mega session. From what I understand there were good points on both sides. Just like anything anything else we're told by physicians, we're relying on them to use their professional judgement. If a Dr. uses Artas on a patient that isn't a good candidate for it, it's probably not a good thing.
Also in my case, the number of punches from Artas were less than the number of actual grafts inserted (Artas took about 2000 punches, but the number of grafts were significantly higher because of course the technicians split some of the Artas extractions into more than one graft).