Even before Let's Encrypt was a thing, that is how most DV (Domain Validated) certs were issued. It was just a more manual, more expensive process to do it. GP's point is since the system depends completely on trusing the DNS chain anyway, why not have the registrar [sic. it should actually probably be the registry] act as the CA as well and cut out the middleman, and the need to verify the domain from multiple paths to prevent MitM.