As Compressor Stall alluded to, when I first read the report, I had to re-read paragraphs to confirm that it was in fact a single pilot operation and that a second crew member had not materialised out of the ether.
Being a technical report setting out the facts as determined by the investigators, accurate descriptions and terminology should take precedent over the push for "gender-free plural pronouns".
But in their rush for "gender-free plural pronouns," the ATSB overlooked the fact that there was only one pilot.