The advantage of containers is that they're dirt cheap, universal, and disposable if necessary. In general, they're rigid enough (thanks to the corrugated metal sides) but as cheaply built as possible (using thin metals).
They are uninsulated, can be air tight, but not necessarily air tight, nor water tight for that matter. But the do need to be weather resistant.
I can see how a space container may have a minimum requirement of being air tight so as to be able to survive vacuum, and possibly lightly insulated. This is only in order for the containers to potentially survive transfer in vacuum, not necessarily for them to be able to maintain long stays in vacuum.
With all of these lack of inbuilt infrastructure, containers rely upon the host ship for environmental support. If you want refrigerated containers, put them in a refrigerator rather than installing and maintaining individual coolers on individual containers.
Naturally, the true definition of the container is its size, and handling conditions. Thus being able to be stacked and secured and handled generically. There are certainly load conditions as well (I imagine the container system is not designed to handle containers filled with lead, there's some kind of maximum weight allowed, as well as dimensional requirements).
At the same time, if you wanted to make an insulated, self powered, container that can leverage the existing transport infrastructure, that can be accommodated.
The modular concepts are all too expensive to simply manage holes in space filled with stuff. A modular ship, unloaded, will have (possibly) less volume, and less weight than a ship with a large hold designed to carry regular containers.
At the same time, the individual modules will weigh and cost more than the containers, thus leaving them sit around on a starport tarmac, either filled or empty, is a waste of money and resources. And in the end, the loadout of a modular ship will have more weight with less total volume than the loadout of a container based ship.
Containers are cheap enough to just leave in stacks as they put the burden of structural infrastructure on the port and ships (thus no power, no armor, no insulation, etc.). You can't run out of insulated containers because there aren't any. They're literally all the same and produced by the zillions, making them very versatile even if they represent the lowest common denominator of the needs for transport.
Modular ships make sense for different roles of the ships, but freight isn't one of those roles (at least not mainstream), and it's also why the modular components show up on something like the modular cutter. You don't necessarily see a ship that can take a passenger module or a freight module. If there's that much of a need, a specific ship will fill it cheaper, more reliably, and more efficiently than a modular one. And businesses love cheap and reliable.
