Hello,
Honestly I have never worked on 'Lets Encrypt'.
However considering EX Switches can generate CSR & install the identity/CA chain provided by the CA, even 'Let's Encrypt' should work.
If you are generating CSR outside of the box using 'ACME client or some similar tool', you can simply install the PKCS12 which has identity certificate, CA certificate (chain in case of SubCA) + key pair.
Regards,
Rushi