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The most efficient way to register a large number of on-premise instances in CodeDeploy is by using 'register-on-premise' with role ARN. This approach allows multiple instances to be registered at once with the appropriate IAM role, which has permissions to access CodeDeploy and related resources. Using a role ARN provides governance and security controls, as it ensures that only the expected instances can interact with the CodeDeploy service, following the principle of least privilege.

This method is preferred for scalability, as it eliminates the need for individual registrations for each instance, significantly reducing the overhead of managing these registrations manually or programmatically with less efficient commands. Additionally, using a role allows for automation and integration with other AWS services, making it easier to manage deployments in a dynamic environment.

In contrast, the other methods would involve more manual work, risking inconsistency and operational inefficiency when handling a large fleet of instances. For instance, using the 'register' command for each instance would be labor-intensive and less manageable. Manual registrations via the console would be highly impractical in a large-scale deployment scenario. While registering using a user ARN might work, it is generally more beneficial to utilize roles for permissions management, especially when dealing with a multitude of instances.