I know that. But presumably, Let's Encrypt could participate in a MITM attack since they can sign another key, so that even the visitor who knows that you use them as a CA can't tell there is a MITM. Checking multiple signatures on the same key could raise the bar for a MITM attack, requiring multiple CA's to participate. I can't be the first person to think of this. I'm not even a web security guy.
It might be interesting for ACME to be updated to support signing the same key with multiple CA's. Three sounds like a good number. You ought to be able to trust CA's enough to believe that there won't be 3 of them conspiring against you, but you never really know.
The signing keys used by the Certificate Authority to assert that the client (leaf) certificate is authentic through cryptographic signing differ from the private keys used to secure communication with the host(s) referenced in the x509 CN/SAN fields.
This problem was solved in the mid 2010s by Certificate Transparency. Every issued certificate that browsers trust must be logged to a public append-only certificate transparency log. As a result, you can scan the logs to see if any certs were issued for your domain for keys that you don't control (and many tools and companies exist to do this).