Perhaps the notion of the Auto Train having discounts for round trip bookings is simply due to the choice of dates - return trip obviously at a later date and maybe (but not necessarily) a lower bucket for the second half of the booking because more rooms are available?

Or, conversely, a higher bucket for the first (earliest) half of the booking because* fewer* rooms are available?

Then too, two separate one-way bookings for a car are 2 X $250 = $500 but for a round trip the car is $48 less at $452.

But whether or not that portion of the booking for just the passenger is discounted for a round trip would take a bit more snooping.