Our discourse setup has working reply by email. It seems the mails generated by the assign plugin don’t have the option to reply to the topic by email.
In the plugin options there is a setting called assign mailer enabled --> When enabled, the assigned user will receive a notification email on each assignment only.
The screenshot below shows an example of the mail I receive when someone sends a private message. It says at the bottom of the page that I can reply to this email to respond. I get the same results when I get a mail about a topic.
When someone assigns me I receive a different mail. It only gives me a link to click on, and not the reply by e-mail option.
I was confused. It seems that Troy by mail is working. Did you turn on assign mailer enabled? And still the assign messages do not have the option to reply?