Paid Memberships Pro allows for custom functionality to be added to the email templates add on by checking for templates in other places. This recipe adds a path to your custom plugin and alerts PMPro to check for the folder you've created in your plugin.

pmpro-email-templates-in-customizations-plugin.php

<?php
/**
 * Create a folder in your Customizations plugin called 'email'.
 * Alert PMPro to check the folder in this plugin for PMPro email templates.
 *
 * Custom Function to create a new path for PMPro to check for email templates.
 *
 * @param  array $default_templates Pull in existing email templates
 *
 * @return array                Return the list which now includes yours
 */
function pmpro_email_templates_in_customizations_plugin( $default_templates ) {
	$default_templates[] = dirname( __FILE__ ) . '/email/';
	return $default_templates;
}
add_filter( 'pmpro_email_custom_template_path', 'pmpro_email_templates_in_customizations_plugin' );