Adds an Additional JS control to the Customizer and outputs the JS in the site footer.

customizer-additional-js.php

<?php
/**
 * Additional JS Customizer Control
 *
 * @author    Lee Anthony
 * @link      https://seothemes.com
 * @copyright Copyright © 2018 SEO Themes
 * @license   GPL-2.0-or-later
 */

add_action( 'customize_register', 'prefix_customize_register' );
/**
 * Adds an Additional JS setting to the Customizer.
 *
 * @since  1.0.0
 *
 * @param  $wp_customize
 *
 * @return void
 */
function prefix_customize_register( $wp_customize ) {

	$wp_customize->add_section( 'custom_js', array(
		'title'    => __( 'Additional JS', 'textdomain' ),
		'priority' => 190,
	) );

	$wp_customize->add_setting( 'custom_js', array(
		'type' => 'option',
	) );

	$wp_customize->add_control( new WP_Customize_Code_Editor_Control( $wp_customize, 'custom_html', array(
		'label'       => '',
		'description' => __( 'Add your custom JavaScript below', 'textdomain' ),
		'code_type'   => 'javascript',
		'settings'    => 'custom_js',
		'section'     => 'custom_js',
	) ) );

}

add_action( 'wp_footer', 'prefix_customize_output' );
/**
 * Outputs Additional JS to site footer.
 *
 * @since  1.0.0
 *
 * @return void
 */
function prefix_customize_output() {

	$js = get_option( 'custom_js', '' );

	if ( '' === $js ) {

		return;

	}

	?>
	<script type="text/javascript">
		jQuery(function ($) {
			"use strict";
			<?php echo $js . "\n"; ?>
		});
	</script>
	<?php

}