I guess it depends on where Engineering really is. If we accommodate the forward-extending, matted-in corridor seen in ST:TMP, we have to move it backwards quite a bit, meaning the cargo hold ports now become "directly below". And there's a turbolift right there next to the docking port, while its location relative to the torpedo deck port is less clear.
Plus, the torpedo deck port has this annoying habit of disappearing on occasion! (See the close-up when Kirk removes the
Reliant's nacelle.)
So the question becomes; Are they all from the Botany Bay? Or are they all 'current'(23rd century) technology? Or are they a mix of both?
I guess there's nothing going against the container design having remained unchanged since the 20th century (even though we didn't see it appear in ENT). But why would Kirk have gone back for those things? Khan cut the tractor beam when the two ships were nowhere near Ceti Alpha, and he supposedly took with him everything he thought he needed.
Heck, we don't even know if Khan ever wanted to colonize anything. For all we know, his plan all along was to float aimlessly and broadcast an SOS, then hijack whoever came to help him. The "
How long?" question would be highly pertinent to such a plan...
OTOH, we know Kirk is well stocked to assist random colonists. In "Devil in the Dark", there's this substance they use for making shelters... One wonders why this wasn't used here. Or perhaps the foundations for the containers were built out of that stuff, allowing the bottoms to be knocked out and explaining the greater interior height evident from the sets, in contrast with the ST:TMP direct comparison between containers and people standing next to them?
"Space Seed" and its aftermath are issues somewhat separated from the shuttlecraft topic, as Kirk would have wanted to make sure Khan had no access to spacecraft at any point! That is, the supermen were no doubt beamed down rather than allowed to ride aboard shuttles. And if their containers were taken down by a workbee, then the implication would be that workbees really are worthless as spacecraft...
Timo Saloniemi