Thank you for carefully reviewing the repo and demo; this suggestion is very insightful. Currently, the node sidebar already has a context list grouped by material, reference, and dialogue, but it's collapsed by default and doesn't directly exclude content. Your suggestion to "make the list an explanatory layer" perfectly points out the missing element.
I also agree that Weave and Condense are easier for new users to understand than simply removing connections. The diagram can continue to serve as the underlying structure, while the sidebar answers the question more intuitively: "What content will be used in this answer?"