gnus-alias allows you to set your identity based on the headers in the message you are replying. This is an essential feature in a mail client for me, I want to automatically reply as the person an email was sent to for certain addresses. This does not work in notmuch. gnus sets the variable message-reply-buffer when it sets up a message, which gnus-alias uses to go grab headers. It creates a buffer named *gnus article copy* which contains all the headers and the message body. It seems notmuch does not set this variable when it sets up a reply.
Here is an example of a rule needed to do this. (setq gnus-alias-identity-rules (quote (("work" ("to" "work at example.com" previous) "workidentity"))))