Re: From the description of the technology
Comparing clocks is relatively easy, mostly they operate in the MHz or GHz region so you can look at the phase difference and that can be measured with great precision.
For example, in my own work I compared two 10MHz frequency references by mixing them with a 10MHz + 15Hz oscillator (also OCXO based) and then the two 15Hz results I filtered and then used cheap-ish reciprocal counting frequency counters (TTi-AMI TF930) to measure the offset to 6 digits (so 0.000015 Hz or so) and as that is relative to 10,000,000 MHz I could see differences of the order of 1 second in 21,125 years in terms of short-term wander. And that was all for under £1k in hardware!
If you ever have to adjust the reference oscillator in some bit of test equipment then the simple choice is to put that and an off-air GPS disciplined reference in to an oscilloscope in XY mode and watch the Lissajous figure. If it takes 5 seconds to flip that is 10 seconds for one cycle of error, and for the usual 10MHz that is 0.01ppm error, etc.
Now doing the same for state-of-the-art sources is a lot harder, but the same principle applies!