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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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You do realize that uses multiple vantage points to verify, correct? So, yes, if you're hosting provider or their ISP intercepts requests, you're screwed, but IMO, you need a new hosting provider/ISP if this ever happens.
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It's 2 vantage points in practice. I've been fiddling with it a lot recently especially since I had to work out how to deal with it + DNS round robin. Internet routing decisions aren't made securely. It really doesn't have to be your hosting provider / ISP or theirs doing it.
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There was recent drama about a CA which fairly recently was caught not enforcing CAA and seemed to do all of their security checks via humans manually checking all of the information so... yeah. Also, that CA had a bunch of sub-CAs that were basically regional Spanish goverment.
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