https://iag.dgfi.tum.de/fileadmin/IAG-docs/Travaux2013/08_BI...
[1] https://webtai.bipm.org/ftp/pub/tai/Circular-T/cirt/cirt.409
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.
Maybe.
https://www.arxiv-vanity.com/papers/1501.00996/
https://ui.adsabs.harvard.edu/abs/2021nova.pres.8631W/abstra...
1. Generally for precision clocks you need "cold" or "ultracold" atoms (essentially random doppler shifts of hot atoms kill your accuracy). This means something like microkelvins - this is hard to prepare quickly. And atoms are constantly lost/heated due to collisions with stray gas molecules, even though the pressure is usually something like a quadrillion times lower than atmosphere. There's research into continuous ultracold atom sources, and you could prepare way more than you need and siphon a few off at a time, but both are technically challenging.
2. The way these clocks work is essentially you have some laser, and an atom that only reacts to laser light of a very specific frequency. If the laser frequency is off from the exact frequency you can tell. A variety of effects means that the measurement process takes some time. It's like trying to accurately measure your heart rate in 1s vs 10s - a lot easier to do in the latter case.
Nothing fundamental, just technically quite painful.