I also just noticed the free stopovers no longer seem to work - very sad.
The best used to be great back in the day of paper tickets, I would book WAS-NWK (23h)-NYP (23h)-BOS or vice-versa if I had one trip calling on both NYP and BOS. This would allow me just under 48h in NYP before continuing on to Boston without any incremental charge vs. not having a stopover. I am sad to see this disappear.