Most of the individual boxes you see are empty, the trains are on the shelves. About half of the set boxes have trains in them, others are on the shelves. I never seem to have enough shelf space.
One of the 116 double City Stations I had put away, because a previous owner had painted the roof black. It was otherwise very nice, but it did not display well. I recently got another 116 that just needed cleaning, got the idea to "double-stack" them to cover the black roof. I may try to justify the upper station by running an elevated CTA train past it, if I can find room for the trestle supports.
Your reference to selling the tank car box.......some boxes are worth more than the train inside.
Years ago I went to a Stout auction that was all a west-coast collector's EMPTY boxes. I remember that the prices were going so high that Greg kept reminding us that the boxes were EMPTY, no trains. After the auction I talked to the collector who's boxes these were and he figured that the trains that he still had were almost free, now that he sold the boxes.