2019-09 and 2020-12 both allow "$schema" alongside an embedded "$id". 2019-09 states that all such embedded "$schema" keywords SHOULD have the same value as the "$schema" in the document root, but 2020-12 allows changing it, which requires some finagling when it comes to validating schemas against their meta-schemas.

Changing the value of "$schema" in an embedded resource is an unusual use case and, AFAICT, not understood by most people much less supported - it was meant to support complex bundling use cases, and one can always un-bundle the schemas to work around lack of support. Raising a NotImplementedError with a clear message would probably not be unreasonable. The JSON Schema test suite does not test this functionality at this time.