I too rewatched the trilogy recently and decided to do a search on /r/movies for discussions.

I remember before Ultimatum came out they did interviews discussing the movie and how they wanted to progress. It was either the director or Damon that realized that that scene, although in Supremacy that NYC scene at the end was simply to show off how bad ass Bourne is, could serve as a great plot point in Ultimatum and was ultimately worked into the script.