@Patrick,
Thank you for your deep test. You have right, but if a category is on Off, it's supposedly all his other must be on OFF. In this case, there is no problem.
But you have reason if inside an Off category there is a category on On, in this case, the product is displayed.
About the products attributes, the system must be rewritten in the future, no delay on that. it could be an on next release, now, like always, the focus is to discover the bugs.