Yes, ‘Allow’ applied to taxonomy IDs hides not only posts without allowed taxonomies, but the not allowed taxonomies too.

About users which don’t see any post. Check if there are posts with taxonomies (except prohibited IDs) which these users can edit. URE Pro hides from a restricted user any post, which this user can not edit.

If such post exists, can be edited by a user, but it’s not shown to a user according to edit restrictions you set, can you send me a little example of your posts, user permissions and edit restrictions set for him, in order I can reproduce an issue at my development environment?