The idea is that all the lights on a given building should flash together. That way, an aviator can visualize the solid space between lights that blink the same way. Blink same? Don't fly. Blink different? That's a gap.
And that's how it worked for a while. A building's owner would wire all the lights together and feed them with a centralized oscillator signal.
Later on, when wire got expensive and buildings got taller, they switched to short-range radio, with one transmitter sending the blink signal, and each light having a receiver in it.
This worked fine, because all oscillators will drift eventually, so every building gets a different blinking pattern.
Then GPS happened.
Now you can buy a beacon like this one, which is standalone and has a GPS receiver in it. Anyone who's cobbled together an NTP server will know that the GPS system can provide microsecond-accurate time as a side-effect.
So these beacons don't care where they are, but they all know exactly when "now" is. And they can synchronize to each other by synchronizing to the GPS signal. It makes maintenance _so_ easy.