Same for me. I feel like the essay makes some good points about the type of people who gravitate towards middle management, but I'm unable to make the connections myself because the essay jumps around. I'm still confused -- is Matt Cutts the "idiot running my engineering org"?
I think this could and should be a lot clearer, but I doubt it.
When you're bad mouthing your former boss, you usually don't state their name. Even better if you can leave the circumstances ambiguous enough that few people can guess.
If you do name them, that's scorched earth. I'd expect a lot of clear anger directed towards Matt if he was the idiot.
So I read it as her having a good working relationship with him, he was just impressed how much certain scenarios always involved her.
Yes, I also didn't think there was much ambiguity as to her relationship with her boss - a risk averse manager wouldn't have laughed off her situation or enabled her to continue on with her continuous outreach - she would've been deemed long ago as a trouble maker to confine. The point of him laughing it off anecdote is to show the trust in their relationship.
My read is that Cutts is several levels above her (all the way at the top, perhaps), and by contacting the FBI she was doing the job someone in the hierarchy between them was supposed to be doing but avoiding for some reason or other. And the "only you" comment by Cutts indicated that it wasn't just the people in line between him and her, but all over the organization that would avoid contacting the FBI.
link: https://allenai.org/olmo