Intuitively, when I see "Add OU Filter," I think it means that entries would be filtered from scanning in the same sense that you would see the word "filter" in firewall configuration. This is the opposite of how it works.
Since entries are placed in a table with a title "Only scan these OU paths" could there not be a second table that says "Do not scan these OU paths"? In my situation, I want everything scanned except one or two OUs. To add every OU that I want scanned would be counterintuitive and more work.