The idea of color trails is intriguing, and one I'll have to think on. As a note though, the other two handbooks would have their table of contents on different pages, so there wouldn't be multiple navigation templates in that respect.
The "List of navigation templates" was not really intended for end-user use. The idea was to have links to the navigation template for editors, to reduce the number of clicks necessary to edit a navigation template.
Though I could see why it might be confusing for current users.
Whether we change to the Quick Action Links proposed will depend on if we decide on the revised organization for the handbook itself.