Just to clarify the issue, is the "Bob Category" a link category or regular category?

As you said, this is a viewing preference issue and not an access issue. Setting that viewing preference is really outside Role Scoper's functionality. That would typically be handled via template code passing the appropriate include or category argument into get_bookmarks(). If you are doing that and think Role Scoper is overriding the args, then we might have more to talk about.