As of now, for testing, the two WR endpoints are sitting on the same desk with 50km fiber in a thermal chamber (simulating temperature changes in the soil), but in future they will be separated indeed.

The standards-compliant endpoints do all of the work. They count clock cycles for ping pong messages and share with each other the length of time so time-of-flight is tracked and compensated for.

Run 2 or 3 separate concurrent sync's and statistically compare the resulting clocks, for example.