Right now CT support is rough for things outside of browsers; it's a pretty fair bet that if you pick up a command line tool or library, it is not checking SCTs, and that makes those workflows vulnerable. If we flipped that, and the average command line tool or library did validate by default, it would dramatically alter the risk calculus for attackers.
I agree that more SCT validation across the ecosystem reduces the value of a mis-issued certificate to an attacker, but a lot of value still remains.
If 90% of clients did SCT validation, an attacker can still succeed against the 10% that don't, there's no herd immunity.