These disc-shaped tokens are used in Esmer Shuttles, which can't take off without one of these.
When Twinsen is escaping from Zeelich to Twinsun, he needs to get a token in the Astroport Tower of Otringal in order to take off in a shuttle. The same situation is presented when Twinsen needs to use the emperor's shuttle to go from Island CX to Otringal.
Inventory Description[]
"The travel token allows to program the destination of an Esmer shuttle. Without it, the spacecraft cannot take off."