While I don't necessarily disagree with your points when it comes to O/D passengers, I think the story changes when you are talking about connections. For example, I do think the door-to-gate setup at T5 is a bit of a PITA when I am flying to and from London, but I very much value the lounges, the food options, and even the shopping when I am connecting.

The challenge for DL at JFK, much as it was for BA at T5, is trying to balance the needs of the O/D pax with those of the connecting pax. I mean, I don't think anyone is under any illusions that JFK is being built up primarily to attract O/D traffic, but I wouldn't be shocked to see maybe 50% of their International seats filled with connections, so they do need to put some emphasis on the connecting experience. Personally, I think the plans look like a reasonable compromise between O/D and connections.

Finally, I would note that a lot of O/D pax do choose to arrive early. Whether that is due to inexperience, safety margins for those traveling long distances or in traffic, those traveling around meal times who want a decent bite, or just a preference to not be harried, I'd wager that such travelers make up a majority of O/D passengers at the airport. It is fine to consider those that want the fastest door-to-gate experience, but if such pax are in the minority of your base and (most importantly in the NYC context) lack appreciably better competitive options, you shouldn't go overboard in tailoring your product to suit their needs at the expense of other considerations.