Similarly to vaccines, part of the magic is that you don't need "all", you just need "most".
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.