You might be asking whether BreezeJS offers a mechanism for handling arbitrary service calls between the client and the Web API running on the server ... in the manner of the DevForce "invokeServerMethod".
BreezeJS does not . The DevForce "invokeServerMethod" is helpful when you need to talk to the server for non-data reasons. You don't have to open and secure your own channel; instead you can share the DevForce secure data channel between client and server. It's also a convenient way to sent a package of entities. Setting up your own independent channel is not much fun.
But writing and communicating with a Web API service endpoint is much easier. Our thought is that you can manage your non-data communications quite well without the help of the BreezeJS EntityManager. So we don't see the need to implement the equivalent of "invokeServerMethod"
However, perhaps you have a scenario that would cause us to reconsider. We'd love to learn more.