I'm probably not going to state this exactly as it should be but... going back to the original question, if I understood the show correctly, in the original ST there was an episode where they traveled in time twice, and when they got back Kirk told Chekhov / Sulu to check for what amounted to a standard time signal from Star Fleet. They quickly figured out they had arrived back 2 days before they left.
My point is, it sounded to me like there was a constant (sub space) signal from some place they used to set some form of universal time similar to Greenwich Meantime that all of Star Fleet used to keep everyone on the same page.
Like wise, each planet would broadcast a constant signal that acted like a lighthouse. Ships would search for the specific signal for a particular planet (like an ISP) and would follow the signal to the source, even if it was in motion like tracking a GPS in a moving car pinging off different towers as a car travels.