Another example: sometimes there is a stock ticker near the top of the front page, and the number of digits it displays changes as the ticks go by. But they did it wrong, and when this happens the entire layout jumps. I learned how not to make this kind of mistake near the beginning of my self-education in amateur web design.
I can virtually guarantee you that NYT has spent thousands upon thousands of hours optimizing and multi-variant testing their headline display to maximize conversion. In other words, if they followed your advice, they would be leaving money on the table.
As for your stock ticker display bug, keep in mind that NYT likely employs hundreds of developers and dozens of teams each owning various pieces of the website. Bugs will make it to production, so it's a matter of prioritization. I'd be shocked if they weren't already aware of that bug. It's probably lower on some specific team's backlog than a bunch of stuff that will be more valuable for the company in terms of revenue.
Would love to see something that does everything the NYTimes does that is clearly and obviously "better."