As I understand it, if you come across a certificate signed by a CA that claims to follow CT, but isn't in the CT logs, it's a fairly major red flag - at the very least, the certificate has been mis-issued. If the third party _does_ log it in certificate transparency, a site owner can check if any certificates have been issued that they did not ask for.
Question for those with a fuller understanding: How can a browser verify this without leaking knowledge about every SSL certificate (and thus a significant percentage of browsing history) they have seen?