On many of the routes, the car and drive pay both ways, while passengers only pay at one end. That's true for example of the busy Edmonds Kingston run. On the San Juan island runs, fairs are collected only at Anacortes.
This PT-Coupeville sentence makes some sense when considered as a deviation from common practice. They are just saying, that in contrast to other runs, everyone pays in both directions.
It sort of confused me on the last Edmonds trip when they asked if I wanted a round trip. I don't recall that being asked before. Anyways I said no. It was a day trip from Edmonds to Port Townsend, with a spur of the moment decision to return via the Coupeville and Clinton boats. I'm not aware of any discount for choosing round trip versus one way (where that's a choice).
From other route pages:
Passenger and vehicle/driver fares are collected at Edmonds, while vehicle/driver only fares are collected at Kingston.
Passenger and vehicle/driver fares are collected at Anacortes, while no fares are collected at Friday Harbor.
No fares are collected at Vashon Island, while passenger and vehicle/driver fares are collected at Fauntleroy.
In any case, fare calculator should take those details into account, and give the correct fare for the direction that you are traveling.
Regarding reservations on the PT-C run. I've taken it several times without reservations, and the boat was half empty. This last time it was on a winter schedule with only one boat, and 2 hrs between crossings. He warned us at the toll both that without reservations we might not get on. We heard the dock worker conversing with the boat crew, telling them there 3 cars still to be loaded, a Prius C, Element (us) and some other small car. They squeezed us in on the end of the boat.
They like to squeeze small cars into mezzanines and reduced height decks, leaving the center hold free for trucks and tall RVs. They even give a discount for cars under 14 ft. They may load big and small vehicles in separate orders.
General fare information