Classes CSS (Optional) – how do I reference this in php?

You can access those classes like this:

// where 'Top' is the menu name, slug or ID. But not menu location.
$menu_items = wp_get_nav_menu_items( 'Top' );

foreach ( $menu_items as $menu_item ) {
  $menu_classes = $menu_item->classes;
  print_r( $menu_classes ); 
}