Rational, even if the bean is really changed by passing through the civet, it remains 100% kosher. Digested food becomes דם ובשר כבשרו, but undigested food does not, and retains its own kashrus status. Non-kosher food found in the stomach of a kosher animal is not kosher; kosher food found in the stomach of a non-kosher animal remains kosher. Therefore the same must be true of what is found in the waste from the stomach.
Honey would not be kosher if not for the pasuk explicitly permitting it.
Carnauba wax comes from palm trees, NOT insects, and is therefore kosher without any question.