I hear you and agree with all of that *except* for the AT. That train typically consists of 18 or so Superliners, in addition to 30+ auto racks. Even if there were enough single-level cars to outfit the Auto Train, each consist would be way too long to handle, AND Amtrak would be stuck with a bunch of oddball custom AT Superliners. There are six Deluxe Sleepers (all bedrooms on the upper-level), four Auto Train lounges (former dining cars with special booths and tables on the upper and lower levels), and one special SSL with nothing but tables on the upper-level. That last one is configured that way so that they can serve extra passengers if there are too many people for the *three* dining cars.
TLDR: Auto Train is insane and it would be difficult to change up the equipment.