Estimating the uncertainty is indeed quite difficult. Stability can be measured by comparing two uncorrelated clocks. This is why standard institutes tend to b

Estimating the uncertainty is indeed quite difficult. Stability can be measured by comparing two uncorrelated clocks. This is why standard institutes tend to build them in pairs. Measuring absolute accuracy is a different beast, since two similar clocks will also have similar systematic errors. Of course, one can estimate the magnitude of these errors, but there can always be unknown contributions. It is therefore useful to compare different implementations, for example cesium fountain clocks built at different institutes. Still, there can always be some conceptual problem that affects all clocks in a similar way.