I am sorry, that is not really what we asked for.
Almost any filesystem used on client-side uses a hierarchy, even seafile based libraries.
Your suggestion strips away the hierarchy. We wanted to restricted access, as in "fine-grained" permission on sub-directory level.
Your suggestion would generate a flat view on our document structure, loosing any project/department information. Having them all renamed on a flat hierarchy, causes our employees to scroll down 100 or more libraries, to find the e.g "costs" folder for departmentA/projectG/costs.
I liked the previous invisible approach of yours better. Your latest approach however would be unusable for this use case.