Reading the documentation and assets/data.json, I've figured that the first color, dark blue, requires a Kyanite crystal to activate the second inventory.

Nothing I can do will actually make it work. I've set the color of a Junimo chest with the color picker, tried both left and right clicking on the chest with a Kyanite crystal in hand, actually putting the Kyanite crystal in the chest.

Nothing works. What is the magic incantation to actually get a separate inventory in the dark blue chest?

This seems to be related to zoom settings. Reading the "Help and Suggestions" section of the forums for this mod over on Nexus, others have had problems when using zoom scale factors other than 100%.

In any case, setting it to 100% seems to make it work.