As long as you use on for a bus, train, plane to travel, it means in/into. It doesn't necessarily mean its roof. (Keep it in mind that you get on a bus, plane or train; similarly, when you are travelling, you are on it).
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Sleeping accommodations are considered “Sleeper Service” accommodations aboard Amtrak. As Sleeper Service passengers, you and your sleeping car companions (up to the maximum passenger capacity for your accommodation) are entitled to receive all regular meals as part of your accommodations.