Filter the pmpro_pages_custom_template_path later to add our custom file for checkout.php.

pmpro_custom_override_checkout_page.php

<?php
/*
 * Filter the pmpro_pages_custom_template_path later to add our custom file for checkout.php.
 *
 */
 
function pmpro_custom_override_checkout_page( $templates, $page_name, $type, $where, $ext ) {
	if ( ( $page_name === 'checkout' ) && file_exists( dirname(__FILE__) . '/pmpro-multiple-memberships-per-user/checkout.php' ) ) {
		array_splice( $templates, 1, 0, dirname(__FILE__) . '/pmpro-multiple-memberships-per-user/checkout.php' );
	}
	return $templates;
}
add_filter( 'pmpro_pages_custom_template_path', 'pmpro_custom_override_checkout_page', 10, 5 );