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There are validationmethods / accounturi extensions to CAA and Let's Encrypt has an implementation of them for their staging service already. It allows you to force them to use only specific validation methods and by pinning the account URI you can make HTTP(S) validation secure.
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I think Let's Encrypt would deploy it to production pretty quickly if there was more chatter about it. It's not a widely known feature so there's very little push for them to finish deployment. It's odd for something to be stuck in staging for so long. Can test it already though.