The server makes use of the classes VDBService and RuntimeVDB to manage all of the service interaction and VDB updates. From embedded's perspective all that is happening is the ModelMetaData map of sources is being modified. Unless the vdb deployment based upon the ModelMetaData objects is used however, we don't provide good access to the live runtime metadata to make further modifications. An indirect path would be to extend the EmbeddedServer and use the VDBRepository to obtain the VDBMetaData to get at the ModelMetaData.
It probably makes sense for the EmbeddedServer to provide an implementation of the AdminApi moving forward.