Thanks, David, for your continued help. I believe I have sorted this out and 
just
wanted to note what I found here for posterity in case others looking at the
archives have my same question.

Once I determined that indeed my issues with Content-Transfer-Encoding and
Content-Type headers happened with message-mode outside of notmuch, I read more
about how message-mode, MIME, and the rest of the sending chain all work
together. The problem seems to be that I was sending simple test emails to
myself that had only ASCII characters. Despite my own utf-8 encoding,
message-mode recognized that the files only had ASCII characters and set the
Content-Type header as just "text/plain" or "text/plain; charset=ascii" (still
not sure about the charset aspect). And with only one ASCII-only plain-text
part, Content-Transfer-Encoding was not necessary and therefore not set. When I
use a utf-8 character (e.g., Süßwasser), both the Content-Type and
Content-Transfer-Encoding were correctly set.

Thanks again for the tremendous software and help.

Yours kindly,
HGV
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