When you create any stream with JSON_SR, the deserializer will make a request for the most recent version of the subject (based on topic name) in the Registry. You can override the ID, but otherwise, it is never fetched for every record, as it would for a regular consumer. This mechanism is what allows ksql objects to have a static schema, and therefore cannot support multiple schemas within a topic. For that, you must move down the “Kafka abstraction funnel” to Kafka Streams, or consumer API.
As always, search github issues before asking. Support multi schema topics · Issue #1267 · confluentinc/ksql · GitHub