Currently the buildkite agent KMS support is limited to (as per the environment script)
aws s3 cp --sse aws:kms source destination
which ends up employing the default master key for the S3 service, i.e. the key that is used to encrypt S3 objects when no other key is defined.
It would be ideal to make use of an explicit kms key id issued exclusively for buildkite agent purposes. Something like
aws s3 cp --sse-kms-key-id arn:aws:kms:ap-southeast-2:123456789:key/ac54dbd2-f301-42c1-bab9-88e6a84292a9
where the arn for the key could be passed in as a parameter to the Cloudformation template for the stack.