I know it is possible to configure replication factor these internal topics for the kafka streams, our application uses for normal application topics with replication factor 3 b
Yes, you'll want to use the same replication factor of your application topics for your changelog/repartition topics.
You can specify the replication factor your changelog/repartition topics via
properties.put(StreamsConfig.REPLICATION_FACTOR_CONFIG, 3)
HTH, Bill