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UPDATEL: for now, the most number of that variables is placed in the parseContent method of the BxDolEmailTemplate.php class. The email header and footer keys have the following syntax:
'email_header' => getParam('site_email_html_template_header'),
'email_footer' => getParam('site_email_html_template_footer'),
it means the header /footer form the Polyglot section.