Basically, CT did indeed worked as designed, but there was no monitoring by the domain authors (which to be fair there are a dearth of solutions of the time).

On a related note, Let's Encrypt also issued the presumably-interception certificates. This can be possibly something that requires interception at the VPS level (otherwise we already detected the BGP leaks). Presumably, Hetzner was forced to do a raw interception and then redirecting all relevant ports to a middlebox for inspection and CA issuance (and since that the ACME spec is well-defined, they can simply check if the handshake contains the TLS ALPN challenge and then redirect them to special code that will reply with the correct things).