In order to customize e-mail template for Woocommerce E-mail customizer it is necessay to make chages in email templates that places in \wp-content\plugins\woocommerce-email-control\templates\emails\supreme\customer-invoice.php or similar templates in woocommerce-email-control plugin.
And \wp-content\plugins\woocommerce-order-status-manager\templates\emails\customer-order-status-email.php for woocommerce-order-status-manager plugin.