According to the American Society of Non-Destructive Testing the unaided human eye cannot discern any measurement less then 1/64". That is the national standard for inspection using a scale. Any measurement below a 1/64" graduation has to be performed using a precision instrument.
I use a quality 48" scale as my shop standard. Every non-precision measuring device is compared to the 48" standard and as long as all of my scales visually agree with my standard that is sufficient for my shop. The 48" standard is never used for production work.
CNC work is unique to itself and I can't remember a time when non-precision work was co-mingled with precision measurements. In other words I never check my CNC work with a scale which I think is what everyone here is saying. Tooling is inspected to determine the actual size and when it is not accurate I make up the difference in my software as many here have suggested. Consideration has to be made to allow for tooling that sees a temperature increase when it is used but that is only in very rare situations, I try my best not to even consider working to machine shop tolerances.
I am well aware of the temperature variation in my shop and its effect on jobs such as inlays particularly when an acrylic male is an inlay into a wooden base or the reverse situation. An acceptable very close tolerance fit in the evening when my shop has warmed up for many hours normally will not fit the next morning when the temperature decrease is just a few degrees. When material types are identical this is less of a problem but its still a concern.