These two patches provide support for features like the one in the subject line. Along with these two patches, I have one for git format-patch (which I will submit upstream soon) that uses the output from notmuch reply --format=headers-only to build a reply with proper referencing, To, and Cc fields.
Since options for git send-email are passed to git format-patch, git send-email --notmuch id:<ID> is a substitute for git send-email --in-reply-to <ID> --to <TO> --cc <CC> --add-header 'References: ...'
