I can use HPKP to pin the cert I get from Lets Encrypt; a cert issued for my domain some other way won’t be trusted due to the hash of its public key being different from the one I pinned.
From https://developer.mozilla.org/en-US/docs/Web/HTTP/Public_Key...:
The Public Key Pinning Extension for HTML5 (HPKP) is a security feature that tells a web client to associate a specific cryptographic public key with a certain web server to decrease the risk of MITM attacks with forged certificates.
HPKP makes administration more complicated but if your threat model includes state-level actors, it prevents them from getting a CA to issue a valid certificate for your domain.
Certificate Authority Authorization (CAA) has been mandatory for CAs since September 2017; it uses DNS to specify which CAs are allowed to issue certificates for your domain: https://blog.qualys.com/ssllabs/2017/03/13/caa-mandated-by-c....