I just wondered today how they moved the cargo containers for Khan & company down to Ceti Alpha V
Unlikely as it seems, they might have been flown down in the configuration we saw used for space maneuvering, with a flimsy "spine" connecting the pods and with a workbee clamped at the bow.
That is, the set was built with the "spine" in place, up to and including the mounting for the (missing) workbee!
It does stretch credibility, though, that the "workbee train" would be capable of such feats. So perhaps we should once again politely but firmly ignore author intent and decide that the bunch of six containers (or, rather, three double-width ones) was beamed down with a cargo transporter, but with the "train" system attached for some unknown reason. Perhaps it distributes power to the containers, and was considered handier than a bunch of cables in that task even planetside? Or perhaps its supposedly feeble maneuvering thrusters can still move the containers across short distances, and Kirk decided to give Khan the option of relocating his camp later.
We are probably supposed to ignore the fact that Khan's containers are slightly larger than the ones seen in ST:TMP. Perhaps the greater interior height can be explained by Khan kicking out the bottom plates and digging pits in the ground, then placing the bottomless containers over the pits (a fairly standard way to build huts in general)?
A dedicated cargo shuttle would probably be a wholly enclosed craft, not placing the "rolling door" corrugated surfaces at the mercy of the elements during atmospheric flight...