How can I include a custom template file in an email template using smarty?
I dont think CiviCRM does this by default
However, I do think this is a good idea and makes sense to include it in core for non-civimail mailings (which already have a header/footer)
Might want to modify the core mailing functions: 


CRM_Core_BAO_MessageTemplate::sendTemplate

to add a default header / footer


Might want to allow this to be overridden both at the system level, function level and via a hook