When using an external Template, the quote header rules from the account are still used, e.g.:

by default, when loading the external template, the quote header of the selected account will be placed before the quoted portion of the mail. The only way to suppress this currently is by deleting the contents of the "Quote Header" field.
A new command %suppressQuoteHeaders% will be implemented to override these account specific settings and remove both the standard quote header by Thunderbird (on 12/3/2010, John wrote:) and the quote header defined in SmartTemplates "Quote Header" field.
This feature will also be useful for issue #173 - the original poster wants to remove all quote headers when forwarding mails.