Themes:
Personally, I would create a “child theme” and chuck in any customizations in there. This plugin does not automagically detect active theme or plugin added menus. Pretty tough to do that across an entire network of blogs, each with different themes and plugins. Only core menu items are listed.
Users Menu:
If the profile sub menu is enabled, it is promoted to the parent menu. Profile promotes to a a parent menu if the Users menu is hidden. Disable all the users menu check boxes and they should all vanish. It does for me with the current plugin and WP4.2.2