Wait, how does that makes nginx use the certificates? For me it doesn't have any cerbot/letsencrytpt specific configuration as I use DNS-01. I just point ssl_certificate and ssl_certificate_key to the correct path where cerbot saves the certificates and be done with it.
Making use is easy as well, like you described. Just a matter of specifying ssl_certificate(_key) path. It doesn't support variables so it can't be based on the server block's domain/variables unfortunately.
DNS challenges are a bit more seamless, but I personally don't like giving access to entire zones to a single machine. Like most DNS APIs force you to.
/etc/nginx/letsencrypt.conf:
/etc/nginx/sites-enabled/default: Reload nginx.Invoke certbot for the new domain once with: