There are plenty of ways you would never be able to tell if a fake cert had been generated and used via this attack vector (let's ignore validation attacks):

1. CT does not do anything if a state actor demands a CA in its borders generate a cert without publishing to the CT logs (or a three-letter-agency doing this illicitly). They can put SCTs in the cert, and still not publish to the logs, nobody is auditing the logs for every cert every browser sees.

2. Browsers won't check for SCTs in certs if they come from a private CA. you can MITM any domain through ZScaler all day long and nobody will notice

3. Wildcard certs make it easy to make/renew a cert that looks normal but hides requests on new/different hosts

4. Non-Browsers do not validate SCTs

I feel somewhat confident in speculating that a bunch of people at large companies will, in fact, be auditing the logs following this. That’s their main value; they’re not really an online/active prophylactic.

“They can put SCTs in the cert, and still not publish to the logs, nobody is auditing the logs for every cert every browser sees”

I don’t think you can get the SCT from a log without the log publishing it? That would defeat the purpose.

“Certificates that support certificate transparency must include one or more signed certificate timestamps (SCTs), which is a promise from a log operator to include the certificate in their log within a maximum merge delay (MMD).[4][3] At some point within the maximum merge delay, the log operator adds the certificate to their log.”