In addition to the other points in sibling comments, even if you use DNS for your domain validation, and use DNSSEC, there is nothing to stop a MiTM attacker fr

In addition to the other points in sibling comments, even if you use DNS for your domain validation, and use DNSSEC, there is nothing to stop a MiTM attacker from requesting a certificate from Let's Encrypt (or some other CA) using the http method.