Since the article title is different now, I assume a moderator looked at it at some point. IIRC, they check all instances of the flame war detector firing, to prevent false positives. In this case, they probably didn't find the comments salvageable.
On the other hand, https://news.ycombinator.com/item?id=19493033 is currently on the front page after previously disappearing, so the mods seem to have intervened in that case.
The lack of transparency with the soft censorship is alarming, particularly given YC's financial conflict of interest.