Not an expert by any means, but I’d guess that has to do with the distinction between being on top of something, and having boarded something. You are on top of a (small) boat or motorcycle, but within a car. These examples refer to position. You can be both in or on a bus, plane, or yacht, because you have boarded the bus, plane, or yacht, and thus are “on” it, but are located physically within the vehicle and so are also “in” it (in the case of a yacht, that may depend on whether you’re inside it or on top of it). These examples refer to both position and state of existence.

This is totally conjecture so I’d be very curious to hear from an actual expert.