But from the comments I see on Reddit, I suspect there may be a simpler explanation: a lot of people for some reason really dislike John Gruber and view him as someone who slavishly praises Apple.
I'm a big John Gruber fan, and I don't think this is true in the slightest. I think he thinks carefully, forms his own opinions, and is very willing to intensely criticize Apple as evidenced by his recent article on the State of Cupertino.
But this means his pro and con opinions don't match typical opinions and this makes him polarizing. And hence some people will flag his articles reflexively or post reflexive dismissals. And Hacker News is heavily weighted to downrank polarizing articles.
I've seen this same pattern happen with other topics where an article doesn't match the zeitgeist, even it the article itself is not flamebait. I think the Something Rotten in the State of Cupertino should have been at the top of Hacker News.
But overall the algorithm has kept HN an interesting place. Any good moderation policy has side effects and tradeoffs.
Dang would be the one to know, but it looks to me there's an innocuous explanation here. As for transparency, it's always frustrating to have it. But transparency in algo's invites gaming of those same algo's (and I don't mean by John). So I wouldn't expect the HN modteam to publish details about their algo.
Edit: since I posted this, the article was flagged. Which I think may support the thesis. I will say the mod team might consider a vouch feature for articles the way one exists for users/comments. I think it ought to take a lot of vouching to counteract flags, but there are clearly articles where this is warranted. The OPSec breach this week was one of them (and it was restored).