John - The freight costs mentioned would have been to get the airframe back to Sydney. Yes, there was a railway from Pine Creek to Darwin, but there was nothing by way of aviation-repair facilities in Darwin, that could rebuild a wrecked aircraft in 1928.
Even if the aircraft was railed to Darwin and managed to be able to be lifted aboard a ship, the cost of shipping by sea from Darwin to Sydney would have been prohibitive.
Selling off the components from crashed aircraft to locals was a common occurrence in the 1920's. Many a time a budding local aviator was overjoyed to be able to acquire a power source for a locally built aircraft from a wreck.
The Silver Centenary:
Silver Centenary - Wikipedia, the free encyclopedia
Anderson and Hitchcock crash in the NT