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It looks like cPanel & WHM version 58 will make it to RELEASE next week, which means this feature will start popping up for more and more of our customers. One of the most highly requested additions to AutoSSL is support for Let’s Encrypt.
We’re also working on adding SNI support to cPanel, WHM, and Webmail. When that’s complete, the free SSLs will allow all cPanel, WHM, and webmail logins to use the domain SSLs, and resolve this feature request. That might not make it until cPanel & WHM version 62, but it’s definitely coming!