First you need to examine the box as a research topic (this doesn't destroy the box), and then you can open it in the workshop. The research only needs to be done once per container type.
A for the Cult of Apocalypse, I am actually working on it right now, but I don't expect to "finish" it any time soon... This arc is a "filler", meaning that it is not required to complete the game, and not even well defined. I have certain loose ideas which I will be implementing as needed/wanted.