mrfloppy wrote:That way people can have custom certificates in an automated, easy and secure way.
It is not a secure way because it's automated.

I don't see by any way how that's not secure. It's probably one of the most secure way to obtain your certificates. You don't have to manipulate your private key and neither the rest of the certificate chain, plus you need to renew once every 3 months. Google do have certificates that last only three months:

And I'm probably sure they automate everything, because it's the most logical thing to do when you have a lot of servers to manage (like they do).
As for your question JollyOrc, use an Apache2 proxy. It will make your setup a little simpler. You won't have to change the configuration of the subsonic web server and it will allow you to centralize the management of your certificates only by using the client command line tool of Let's Encrypt.