Exim and Dovecot do support multi-IP ssl certificates, but their setup can be a little bit tricky to try and maintain.
With LetsEncrypt, we can setup multi-domain certificates for the hostname, and mail domains, all in one value, to make managing SSL for mail a little simpler.
To do this, we use the letsencrypt.sh script normally, but we manually create the ca.san_config file, loaded with the values we want to use.
With LetsEncrypt 1.0.4+, we can specify all values on the command line, like this:
cd /usr/local/directadmin/scripts ./letsencrypt.sh request `hostname`,mail.domain.com,smtp.domain.com,www.domain.com,domain.com 4096