A specific container with a reference ID. I select the container in the cell window and choose edit. Inside that menu I see no way to place items in that specific container vs editing the base ID.
The only way to place items into a specific RefID container is with AddItem - but the container needs to either be a "quest" container or it needs to have the "persistent" flag checked. You can't reference non-quest or non-persistent RefIDs in a script. The downside of using the persistent flag (as I understand it) is that the container remains in memory, even if the parent cell has been swapped out or not yet loaded during this game session.
All special one-off containers are actually separate baseIDs with a single instance RefID somewhere in the world. So, AFAIK, you have to add the items in GECK to the base object and not the reference object. (Which makes sense, because the base objects never actually exist in the game world, therefore they can't actually hold anything, they can only be set with a list of items that will be spawned into existence when the reference object's cell is loaded for the first time. Or, if set to respawn, they can be configured with a list of items or level lists that will respawn into the container when the cell resets.)
Base objects don't exist - Reference objects are the physical manifestation of base objects in the game world.