Quite possibly. And it's not as if the containers would be standardized for stackability or anything. In all of Trek, from TOS to sequels and prequels, cargo has been chiefly carried in the general goods fashion, in separate man-handleable barrels or boxes or cylinders, and the methods of moving that around probably have to be very flexible.
The TMP/ST2 containers could be more like the Trek equivalent of the cargo boxes of commercial aircraft than of the standardized seagoing, railgoing and roadgoing steel containers. That is, something to wrap around a bunch of goods for the duration of a short transfer, and something that is available in many sizes and shapes to fit all possible applications.
McCoy speaks of materials for quickly creating surface accommodations in "Devil in the Dark". Perhaps Khan was supposed to build his own new Khanton out of those, but the sandstorms ate it all away, forcing a move into the set of "baggage wrappings" discarded at the edge of the failed community.