I think this is what you are looking for:
Personally, I haven’t run into any compatibility or stabillity issues running Let’s Encrypt and the other third party things like AppDaemon, Harmony-API, HADashboard, etc.
There have been issue with the new flash briefing though; it doesn’t seem to accept Let’s Encrypt certs. Not sure if that’s going to be fixed (or if it can) but there was a thread on it. Folks were using nginx to get around it but for me it wasn’t worth it.