The majority of international boxes are 40 footers and the bigger wells just take up additional train length and I believe the gaps between boxes add drag and hurt fuel efficiency. I think the gaps also allow people to break into the bottom container.

There is enough space that a 53 footer can still ride above the 40 footer. Trailer Train has had a fair number of larger well cars cut down to 40 feet.

Perhaps the drawbar connected cars are more used for international boxes and the single platform cars for domestic boxes. I have not heard of any single well cars being cut down.