If you page through the /newest listings you can see [flagged] and [flagged][dead] submissions.
eg. this: [flagged] A migrant surge tests Spain's open policies (economist.com) - https://news.ycombinator.com/item?id=49131860
is clearly marked as flagged.
Unlike the current submission: Ten advances in mathematics and theoretical computer science (openai.com) which isn't [flagged].
That's true, but submissions are only killed in that way if they receive a ‘fatal’ number of flags. However, flags lower the rank of a story even at non-fatal levels. What antirez is suggesting here is that the rank of this story has been lowered by flags – and that seems plausible, if you compare its rank to that of other stories with a similar age and number of points.