I suspect the 3 month certs is to make sure you have to authenticate your domain 4 times a year with Let's Encrypt to make sure that you can't hold a valid SSL

I suspect the 3 month certs is to make sure you have to authenticate your domain 4 times a year with Let's Encrypt to make sure that you can't hold a valid SSL key for the domain for more than a few months after you transfer it. Also, if someone manages to scam Let's Encrypt, the resulting cert is only valid for a short time. The local client is there to make sure that the authentication process can be automated and not require your manual intervention.