As for the Auto Train it's probably not that smoking itself is illegal so much as you need to provide substantially separate air supplies and various other considerations. It may be possible that if Amtrak was willing to provide those special modifications on other trains they could have legal smoking wherever they wanted.
Actually Amtrak did provide modifications on all of its long distance trains for a number of years after smoking in general was banned from Amtrak trains. Those modifications went away for two major reasons, abuse by the smokers and a poor design for the Superliner trains.
On the Auto Train, the special rooms are in the cafe cars. This is why one can sometimes catch a hint of a whiff of smoke when in that car despite the best efforts of the design. On the rest of the Superliners, this special room was installed in a coach car. The design of the cafe cars is very different from the AT to the rest of the fleet. In the cafe car if one is bothered by the smoke, while perhaps not totally fair, at least one can leave the car and return to your seat or accommodations. In coach, you can't really walk away from it. And in typical Amtrak fashion, there would on occasion be the Amtrak employee who couldn't be bothered to honor a request from a passenger to move their seat to another car.
However, the major reason that Amtrak did away with these rooms as I mentioned above was abuse. On occasion there would be too many smokers in the room and it would get too smokey. So they'd prop open the door by jamming something into it. That of course then allowed the smoke to travel through the entire car. Additionally, there were a few too many who were slobs. I'm not saying that all were, but more than enough would use their soda cup as an ash tray (instead of what was provided), and then leave it behind. Invariably that cup would fall over and how you have a very sticky mess that is extremely hard to clean.
So thanks to those who abused the privilege, now all smokers pay the price by having to wait until the designated stops.