Can't imagine any way to do this. Remember, we don't even have access to the MIME-wrapped form of the message, just the individual HTML and text parts. Customizing SMTP headers is a step beyond that.
Also, Message-IDs need to be globally unique. What algorithm would you use to guarantee such uniqueness?
But more to the point, as @Kristen M asked, what are you trying to accomplish? If you're trying to hide information from human readers that can be parsed by a machine, you can do this with an HTML comment.