> So the state can now MITM and listen to all secured connections, and the only giveaway is that the cert is not in the certificate transparency log, or if the CA used does not match the domain's CAA record (when it exists).

Or when the domain uses HPKP to pin its certificate to a different CA. When the MITM CA has been added manually to the browser's root key store, most browsers allow HPKP bypass by that CA unless configured otherwise; but if the MITM is done by compromising one of the browser's default CAs, the browser won't allow a bypass.

Or if the certificate was supposed to be an EV certificate, which can only be issued by a limited number of CAs, and the compromised CA is not one of these. And even if an EV CA is compromised, AFAIK some browsers require the certificate to be in a Certificate Transparency log, and they also require that the certificate carry proof of its submission to the CT logs.