That was a unique case in my memory. "Often rank a pro-YC comment to the top of a thread" is pure fabrication. As I've explained many times, we intervene less, not more, when stories are anti-YC, precisely because of the conflict of interest. It's literally the first thing PG emphasized to me when explaining how to moderate HN.
A recent example is https://news.ycombinator.com/item?id=9622711. That class of outrage thread is something we routinely penalize, but we penalized this one less because it was about Airbnb. There's no way it would have stayed on the front page for hours otherwise.
I think strictly speaking that may be true, however I suspect the reason that that is is because of the precautions already taken by the HN software and HN operators, e.g. by rankbanning. When users who have voiced anti-YC sentiments are already rankbanned, for example, you don't even need to intervene, because those comments will already have sunk to the bottom. So I think you can probably successfully refute my individual points but the larger spirit of my assertion remains.
Newer comments are given a boost in rankings so they have a chance to get upvoted. That comment might have been upvoted enough to stay on the top afterward (I am not affiliated with YC or HN).