Hi Michael, I’m the designer for that story.
Normally NYT doesn’t indent paragraphs like that, but here I felt it was warranted given the story’s structure (it’s chapterized), length and tone. Vertical space between paragraphs (like on all web NYT articles) give stories a quick, punchy reading rhythm. In those articles all crucial information is absorbed into first three paragraphs or so. Indenting them (without vertical space) gives them a slower, more patient rhythm, like a novel. It’s uncommon, but again, I felt warranted in this case.
R. Taylor