Here's my general thinking at the moment with the transport container in place. I've only started, but now I can see what I'd like to do differently as well as lengthen it just a bit. The attach collar can be fitted either above or below the container (since there's no real "up" or "down" in space) and the thingies on both ends are for attaching pods together in a train like arrangment such as if needing to move around more than one at a time, Think along the lines of moving around more than one car at a time in a rail yard or a docking yard. But you wouldn't ship them that way in warp flight. A transport variant of the clipper could also carry two more of these containers, one on each side of the aft section, and those other containers could be larger/longer because there's no superstructure on the sides (going aftward) to get in the way.
The transport variant of the clipper is meant to be a fast transport. Other types of ships more specifically dedicated to bulk cargo could probably haul bigger containers.