You can manually make sub-domain certificates
In my script i have the following
./letsencrypt-auto certonly --standalone -d $mydomain1 -d $mydomain2 etc....
So just append multiple domains "-d switch" when you register.
Although i am not really a windows person, it would seem that located at this address is a CLI tool that will also allow you to auto renew on a windows machine.
https://github.com/Lone-Coder/letsencrypt-win-simple
Does this help?