Anypoint Runtime Manager allows deploying Mule applications to CloudHub or on-premises servers running Mule runtime. While the basics are the same, the deployment targets offer different management features due to using different Mule Agents. When deploying to CloudHub, applications use legacy Mule Agent functionality, while deployments to managed servers use new Mule Agent features. The document outlines key differences in areas like load balancing, disk persistence, high availability, logging, and more between the deployment options.