Create the !!custom_message!! shortcode for the Email Templates Admin Editor Add On and set a custom message per membership level.

my-pmpro-email-data-custom-message-per-level.php

<?php
/**
 * This recipe adds a custom email shortcode !!custom_message!! that can be
 * used in the Email Templates Admin Editor.
 *
 * You can add this recipe to your site by creating a custom plugin
 * or using the Code Snippets plugin available for free in the WordPress repository.
 * Read this companion article for step-by-step directions on either method.
 * https://www.paidmembershipspro.com/create-a-plugin-for-pmpro-customizations/
 */

function my_pmpro_email_custom_data_per_level( $data, $email ) {

	// Set a default custom message
	$custom_message = ''; // Optional: add default custom message for all levels, e.g. 'This is my custom message'

	// Is this a checkout email for the member?
	if ( strpos( $email->template, 'checkout' ) !== false && strpos( $email->template, 'admin' ) === false ) {

		// which level is this email for?
		$level_for_email = $email->data['membership_id'];

		// Set custom message per level
		switch ( $level_for_email ) {
			case '1':
				$custom_message = '<p>My custom message for level 1</p>';
				break;
			case '2':
				$custom_message = '<p>My custom message for level 2</p>';
				break;
		}
	}

	// Let's only add the message if it is not already added.
	if ( empty( $data['custom_message'] ) ) {
		// add !!custom_message!! shortcode
		$data['custom_message'] = $custom_message;
	}

	return $data;

}
add_filter( 'pmpro_email_data', 'my_pmpro_email_custom_data_per_level', 20, 2 );