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At the moment, Let's Encrypt primarily issues certificates based on insecure, authenticated HTTP-based validation of domain control. They validate DNSSEC but the HTTP-01 method by itself is insecure and the DNS-01 method requires giving servers DNS API access which isn't good.
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They appear to consistently check from 2 perspectives. If there's an attacker with a MITM to both locations, there's currently no way to defend against them getting a Let's Encrypt certificate until they ship the nice accounturi feature. DNSSEC + accounturi gives secure issuance.
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