It seems as expected behavior. Restriction by category ID is global for all taxonomies. So when you all to see at backend and edit only posts with category (taxonomy) ID=3, you automatically prohibit editing posts with any other taxonomy ID. Thus use can not add to the post new tags/taxonomies.
As about 0 items at the tags or categories page, it is a result of URE’s internal caching. But if you limit user to edit post only with the restricted list of existing taxonomies – you should not allow him to edit them. You have to delegate this function to another user according to my logic. So taxonomy editing pages should not be available to a user restricted such way.