HI Andrew,
This is pretty much speculative but it will also give your question a bump.
Look at metacourses as well. They might be useful in the sense that, for Selected, you could have an initial landing course for each academy that then links to a child or metacourse -- out to the globals and also out to the selected.
OTOH, I think you can sketch out some venn diagrams that would work with cohorts and perhaps not even worry about categories.
Academy A cohort is only in course Default A. Academy B cohort is only in Default B.
All cohorts are in Global.
A and B cohorts are in Selected.
Once a user is in a course, they are typically shown only the courses they are in. It is possible to show all courses and see the course names, but we find that rarely happens, and of course you set the courses so self-enrollment is not allowed.