That's a good example! The topics in question are created by the Kafka Streams client library using the standard Kafka APIs, so it works just fine with Bufstream. The Kafka ecosystem takes a thick client approach to many problems, so the same answer applies to many similar Kafka-adjacent systems.
There are, of course, some internal details that Bufstream doesn't recreate. We haven't seen many cases where application logic relies directly on the double-underscore internal topics, though - especially since much of that information is also exposed via admin APIs that Bufstream _does_ implement.