Prior to the Amtrak buying the current, new auto racks Amtrak had to carefully monitor how many over sized vehicles they booked as there was limited space for them. For that reason, they've always handled booking them separately and just like sleepers and seats, there are buckets for both regular and over-sized vehicles.
The new racks handle all sizes with no need to use special racks for the over-sized cars. However, perhaps because it's too lucrative to change things or perhaps because operations never talks with revenue management, Amtrak still treats things as though they still have separate auto racks for each type of vehicle.
My guess, and it just that, is that no one will care if you show up with a car when you've booked space for an SUV. If they do care at all, it might be that you paid too much, since the buckets for over-sized are more expensive than the corresponding buckets for cars. However, in this case it would appear that the car bucket has been kicked a few times, while the over-sized bucket hasn't, hence your seeing a cheaper price for over-sized.
If you tried to go the other way however, booking a car and showing up with an over-sized, that would definitely be a problem.
