When i want to use features from Designer in Java service, i usually reverse engineer the features using their corresponding jar files in the plugin folder of the Eclipse. From what you are trying to do, you might want to explore the idesignereditor.jar. There are few methods in DestinationComparator class that might help you.
AFAIK, there is no official CLI for Designer that Developers can leverage but i can be wrong!
#Integration-Server-and-ESB#webMethods