The attacks you mention (correctly) base themselves on the security of the signing key used to sign the E3 binary. The security of this key is obviously extremely important, but is only one part of the attestation process. Nitro Enclaves exposes attestation documents with platform control registers (PCRs). PCR8 is a hash of the key used to sign the binary itself, but there are also 5 others which contain hashes of the specific binary that is being run as well as the in-memory state of the enclave. Combining these together, means that attestation focuses both on deployment integrity (and GitHub Actions is the weakest point here) as well as the code itself. This is why exposing the code that runs inside E3 is a major focus of ours.
Re: KMS policy integrity, having the enclave communicate with IAM with TLS certificate validation is one way of E3 proving to the end user providing keys/data that the enclave key has not been tampered with. It's a messy solution, but cryptographically robust assuming that the AWS Root CA has not been compromised.