Works for me. Not sure if adding support for aliases would also be useful like with certbot:
certbot-auto certonly --standalone -d example.com -d www.example.com -d ...
Is there a difference besides having a base domain?
At any rate, I remember getting half-stuck at this stage though (from the README):
After properly testing, open letsencrypt.conf, comment the testing CA hostname
(the LE_CA_HOSTNAME setting), uncomment the production CA hostname, register
your account key at the production server and request the final version of your
website certificate.
"register your account key" wasn't obvious to me, but I believe all I did was do
./letsencrypt -register example.com and then proceeded doing the same for the subdomains. After that I added the relevant keys to their respective VirtualHosts.