Instead of literally translating the edmx:Include element into a sub-object of the translation of the edmx:Reference element make it a property of the "schemas" object that is a JSON reference to the referenced document.
This way all schemas in scope of the service are consistently represented as properties of the "schemas" object instead of just mimicking the XML document structure.
If the edmx:Include element has an @Alias attribute, a second reference to the same URL is generated for the alias.