alt Hacker News> Celestial navigation actually drove the development of accurate clocks
That's true, but that still doesn't change the fact that you don't need nanosecond precision for this purpose. At the equator, 1 second precision gives you roughly 500m accuracy, which is already much higher than what the celestial imagery allows here (4km in the paper).
Clearly this method isn't limited by clock accuracy at all.
1 second precision is a lot. A typical quartz resonator will drift by about .5 seconds per day at ambient conditions. In this paper they set the clock with GPS right before flight and they only fly for a few hours, so it's tolerable. But in a GPS denied environment where you can't set the clock right before flight, ie exactly where you are using this instead of gps, clock accuracy will become the dominant factor affecting your accuracy after a few days.