The first I remember reading about the "Blackbird" was in the _The Uncanny X-Men_, during the Claremont & Byrne run in the early 80's. Their jet was modeled on the SR-71, although I don't recall if they explicitly mentioned that model number.
The Atlantic article that Uncle Bob was writing in response to lists several specific examples of software failures that did, or could have, resulted in loss of life: a failure of the 911 system; air traffic control systems; medical devices.
My interpretation: Assuming the work was outsourced to cheaper laborers (e.g. in India), OP may have felt that his job was at risk. By sabotaging the efforts of those offshore workers and making them appear incapable, he hoped to discourage management from outsourcing that work.
"If DMCA claims were expensive... the garage bands and individual artists/musicians would be left out of the game completely, they couldn't use DMCA to take down their music."
By the end of the article it had crossed my mind that Boyter and Ducker (the perpetrators of the hoax) were themselves fictitious characters, and that the article itself was part of a larger hoax.