Hi Kashif,
The only place I can think of where you can add custom email headers is a custom Email Provider. In it's SendEmailInternal and SendEmailAsyncInternal methods you should be able to do so. Bear in mind this email provider code will be executed for all emails sent in the system and you won't be able to limit these headers only to a specific template. However, you can write some logic based on sender and recipient information which could be helpful.