Earlier quoted context omitted.
The effectiveness of CT logs isn't a thing unless the website uses CT monitoring or is a huge company. A [delegated or non-delegated] DNS takeover, or IP address release (eg. cloud providers re-assigning an IP to another customer) could allow you to generate a certificate for some-forgotten-subdomain.medium-sized.company.com using the ACME http challenge. Of course this is mitigated by properly managing your DNS, and…
Cert pinning mitigates this too right?
IF you pin to an intermediate key, which is under the control of a CA, then bad guys who obtain certs from that intermediate will not be inconvenienced by your pin, but these keys are intentionally long-lived (they are protected in an HSM) so the rotation issue isn't as fraught.