Asi nijak, aspoň v Active Directory:
Most of you have a private PKI within your organization that does not chain up to a public root. In this scenario, CT will not affect your CA's. Chrome browser uses Windows native CAPI to determine trusted chains. Windows can differentiate between commercial/public CA chains and internal/private chains. Since Windows has this ability, CT will not affect Private/Internal PKI chains.
https://blogs.technet.microsoft.com/pki/2018/03/12/how-will-certificate-transparency-affect-existing-active-directory-certificate-services-environments/
Tedy pokud certifikát té soukromé autority není podepsaný nějakou kořenovou, pak se to bude muset řešit i tady.
A jinde asi taky ne, píše se o certifikátech vydaných veřejnou autoritou.
Ostatně, to by přestaly fungovat ty antivirové MITM techniky na on-line kontrolu HTTPS komunikace.