I had this exact same problem when trying to create a program which would email Lotus Notes users.
It has been a while, but if I remember correctly the solution was to send the source in the text portion of the message and include the HTML as a multipart attachment. It was something very odd and hacky, but it solved the problem for Notes. If this is something that you truly need to see in Thunderbird, trying doing a combination of attaching one part and putting the other in the base message.
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