If we're talking interstellar travel, we're likely talking about spacecraft undergoing very significant acceleration and velocity. I'm not a physics expert, but from my understanding it seems that a starship would need to have a very accurate idea of its own acceleration vs reference time curve (relative to some reference frame) in order to calibrate its own ticking clock to the reference frame. For NTP, this isn't so much an issue because on Earth all the endpoints' clocks are all ticking at about the same rate.