By and large referential measuring using a datum point and accurate machine scales will take you where you need to be.
I’d point out that accuracy is not an end in itself, but a property which work should possess only as much as is required, if you’re drilling a bolt circle, then it’s likely to be sufficiently inaccurate due to the process to make laying out to ? a thou somewhat pointless, and if it’s being bored after drilling to achieve that accuracy why worry, the referential method used to position the boring head will make it irrelevant.
Achieving repeatability of tolerances to ?0.1thou (i.e. 2.54μm) or even ?0.5 thou is the realm of second-op work, holes need to be bored or reamed, cylinders and mating surfaces ground, lapped, scraped or planed and so on.
As has been hinted at earlier in the thread, the best thing you can do is to think about the design intent of the piece and which dimensions are critical and require that extra mile in terms of accuracy.