Remove/Disable “Automatically add new top-level pages to this menu”

Since there is no filter to remove this option, your best best to to stick to using CSS by putting the following in your child theme’s functions.php:

add_action( 'admin_head', 'wpse_225635_menu_css' );
function wpse_225635_menu_css() {
    global $pagenow;
    if ( $pagenow == 'nav-menus.php' ) {
        ?>
        <style type="text/css">
        .auto-add-pages {
            display: none;
        }
        </style>
        <?php
    }
}