I think Pull me under is the perfect choice for the encore song for several reasons. Here's my take on it:
1. Performing a really heavy first set and then an entire album as the second set must be exhausting. For this reason, it would be more comfortable and kind for the band to perform one of their less challenging songs at the very end, one that they really don't have to worry about nailing, since they've played it a thousand times. I think James especially appreciates this, Pull me under was probably the easiest song for him to deliver on the last tour, of all I&W songs.
2. The band is still recovering from the venture of performing an entire new album for a whole year of touring. I can imagine the tour took a toll on the band financially and in terms of some fans being put off by it. I don't think the I&W tour completely solved this. Yes, it did help, but they still need to make sure they include something for the casual fans. Not all the fans are familiar with the last ten years of the band, and not everyone that comes to the concert has religiously listened to the entire SFAM over the years. Therefore, it's great to throw a bone to the people that aren't fans of the entire discography.
3. Given that the second set is almost 80 minutes long, it's obvious why the band decided to play only one, relatively short song as the encore. And if you go back through the catalog, there are only a handful of songs that are such smash hits that they work well as being the only encore song. As I am and Metropolis come to mind as the only alternatives, and even the latter is a stretch.