The most common vector for DNS-based attacks on issuance is compromised registrar accounts, and no matter how complicated you make the cryptography, if you're layering it onto the DNS, those attacks will preempt the cryptography.

Because LE keeps a mapping of account ids to emails and public keys. You have to have the private key to the ACME account to issue a cert. The cryptography is still there but the dance is done by certbot behind the scenes.

Prior to this accounts were nearly pointless as proof of control was checked every time so people (rightfully) just threw away the account key LE generated for them. Now if you use PERSIST you have to keep it around and deploy it to servers you want to be able to issue certs.