I took a look at notmuch.el and it uses message-mail hard-coded at a few places. My suggestion is to instead substitute compose-mail, which will honor the variable ‘mail-user-agent’.

Then, the only problem is the function notmuch-reply, which has a call to message-mode hard-coded. I don’t know what to do about that one. Hope more knowledgable minds than mine will prevail.

Maybe message-mode is better or as good as what I’m using today—but it’s still weird to hard-code it like that, and makes it harder to switch to notmuch from other emacs mail setups.

Sandra