I finally got to try out the new method for custom templates. It seems that it finds the template (no warning when submitting the form that it can't find it, $mail->send() is successful), but the part that loads the template doesn't check the custom templates directory. In fact this error goes to the email recipient:
Warning: include(/var/www/pw/site/modules/FrontendForms/email_templates/email_template.html): Failed to open stream: No such file or directory in /var/www/pw/site/modules/FrontendForms/Formelements/Form.php on line 444
Warning: include(): Failed opening '/var/www/pw/site/modules/FrontendForms/email_templates/email_template.html' for inclusion (include_path='.:/usr/share/php') in /var/www/pw/site/modules/FrontendForms/Formelements/Form.php on line 444