How about a dedicated tag for selecting the active theme among a number of installed themes?
I imagine this working the way saved searches work:
My project: - Task 1 - Task 2 ... Searches and theme: - Not done @search(not @done) - Active theme @theme(SodaDark)
I realize this would require an architectural change, not only in the support folder structure, but also to enable the app to render multiple open documents, each with its own theme. But I think it would be worth the work. A research outline might well need a different theme than my todo list, for instance, and sometimes I need to have both open.