It's interesting, if not instructive, that for two years readers have been blissfully unaware of, and presumably not confused by, this usage and that the matter seems to have become an issue only after its somewhat well established use was specifically highlighted to readers.
Could the reason be is that not all reports are read by everyone. I only read the reports that are of interest to me, aircraft type, type of operation etc., It is the first time that I have noticed the use of gender-free pronouns. The reason I picked it up was not the footnote but the the report referring to "the pilot" and in the next paragraph referring to the pilot as "they."
For the last 25 years I have been writing manuals and reports for the aviation industry. When referring to a human in the sharp end, it was "the pilot," "the flight crew" or in a multi-crew situation, "the pilot in command" or "the co-pilot."
It grates as much as using "guys"