You mention it already - bootstrapping. Always optimising, always correcting for yet another flaw in materials, processing, environmental conditions, quality control and usage procedures. Usually, it is helpful that there are multiple ways to do a particular thing that can be used to calibrate each other. Also, there are physical processes that can produce high-quality surface finishes that can be used for calibration tasks, for example by splitting crystals. The resulting shapes are dependent on the crystal lattice, and improvements in material purity reduce any irregularities.
A more general approach is to understand measurement as a process where a minute signal has to be amplified to be more easily evaluated. There are many such methods.
In the case of surface metrology, Coherence scanning interferometry is such a method which uses the properties of interfering light waves to directly visualize surface anomalies as bands of lights. Another, more direct method is to drag a stylus across the surface and to amplify variations in position. Sort of like a turntable does.