Why care about continuous sync? When I was in small robotics startup we had a separate motor controller driving each axis. A customers complained that the precision was getting worse after running for a few days non-stop. Guess what? Each axis had its own CPU clock based timer defining how long a segment should take. The difference is negligible but it accumulates over time. It was no issue for other customers who had a pause somewhere in their motion.

Why nanoseconds though? Usually a sub-microsecond sync is good enough. I can only think of some specialized phase measurements, really, like when you need to know from which direction a radio signal is coming based on timing of two antennas.