Apply the Email Header and Email Footer as set in the Memberships > Email Templates admin page to the WP New User Notification.

my_pmpro_email_template_header_footer.php

<?php
/**
 * Apply the Email Header as set in the Memberships > Email Templates admin page to the WP New User Notification.
 *
 */
function my_pmpro_email_template_header( $header, $phpmailer ){
	if ( strpos( $phpmailer->Subject, 'Login Details' ) !== false ) {
		// only filter the New User notification in WordPress.
		$pmpro_email_header_body = pmpro_getOption('email_header_body');
		if ( ! empty( $pmpro_email_header_body ) ) {
			$header = $pmpro_email_header_body;
		}
	}
	return $header;
}
add_filter( 'pmpro_email_body_header', 'my_pmpro_email_template_header', 10, 2 );

/**
 * Apply the Email Footer as set in the Memberships > Email Templates admin page to the WP New User Notification.
 *
 */
function my_pmpro_email_template_footer( $footer, $phpmailer ){
	if ( strpos( $phpmailer->Subject, 'Login Details' ) !== false ) {
		// only filter the New User notification in WordPress.
		$pmpro_email_footer_body = pmpro_getOption('email_footer_body');
		if ( ! empty( $pmpro_email_footer_body ) ) {
			$footer = $pmpro_email_footer_body;
		}
	}
	return $footer;
}
add_filter( 'pmpro_email_body_footer', 'my_pmpro_email_template_footer', 10, 2 );