@pauloqs As they are cut to a basic shape by CNC and as
@LSchefman says, they are hand sanded, hand finished to ensure the CNC cut marks are removed, they could vary by fractions of a mm. I know the neck joint is cut oversize and then hand sanded to ensure a 'tight' fit and the perfect neck angle. It takes several weeks to make just 1 neck, small work to ensure that the neck is stable and potentially reshaped a bit as the wood settles.
Therefore, the necks must have small variation but also be within a certain tolerance - whether that tolerance is +/- 1/32" or maybe even +/- 0.5mm, I don't know but they can't ALL be exactly the same right down to 0.01mm (or less) after all the hand finishing and settling of the neck over the weeks it takes to get a Neck ready to be married with its Body.
All I can say is that in my experience, with my guitars, I don't really notice a significant difference between my 509 (Pattern Regular) and HBii (Pattern). I do notice more of a difference going from my either of these to my Custom 24 or 594. The biggest difference is my Cu24 to my 594 (and vice versa). The neck difference between my 509 and HBii could be larger than I actually think because there are a lot more significant differences between these two than the neck shape - weight, PU configuration - having that middle PU does make a difference when strumming or picking the guitar. There is also the difference in Scale length - albeit just 0.25" - but also the String gauge - 10's on the 509 and 11's with a wound 3rd/G string, There is also the difference that having a single, fixed bridge compared to the Tremolo bridge on the 509. I could continue but I am sure you get the point that there are far more significant differences than the slight differences in the neck have. When I swap between these two guitars, the other differences are far more pronounced that I am much more aware of than the differences in the neck.
In other words, when I switch between these two guitars, the major differences stand out far and above any small difference in the necks. When there is a more pronounced difference in necks - especially if you are made more aware of those differences - the 'Thin' or 'Vintage' with Asymmetrical carve for example - then those become a 'standout' feature. Maybe if I had more Pattern and Pattern Regular guitars, especially if they don't have too many differences else where, then maybe I would be more aware of the necks. The 'perfect' example would be having a few Custom 22/24's with Pattern Regular and some other solid, twin humbucking, Pattern neck shaped PRS guitars - so the only 'difference' is just the necks. However as I only have 1 example of each neck shape, and there are some really big and much more pronounced differences between my Pattern and Pattern Regular guitar, I am certainly not aware of any 'slight' difference in the 'neck' - not compared to the string gauge and scale length that my left hand, the hand on the back of the neck, notices.
I can also only speak for myself based purely on my guitar collection and my perception. Another person may well find the difference in the neck between my 509 and my HBii too be more noticeable to them but to me, I really don't notice. The differences are still small - less than 1mm and I bet they have a very similar shape too. I also don't tend to be fretting at the nut and/or keeping my hand wrapped around that one area but in playing they don't feel different enough to register with me.