This causes OAS 3 documents that are valid against the spec to fail. (and breaks tooling that relies on the schema for validation)

Here's an example encoding object which fails validation:

          encoding:
            url:
              headers:
                id:
                  $ref: '#/components/headers/id'

The schema should be

          "additionalProperties": {
                "oneOf": [
                    {  "$ref": "#/definitions/Header" },
                    {  "$ref": "#/definitions/Reference" },
                ]
               
          }

I'll submit a PR with this change for you.