Sorry if I'm being thick here, it didn't hit me until afterward. Were those the twin towers in the alternate reality at the end?
Yes they were. The newspaper in Bells office said Obama Set To Move Into New Whitehouse. Apparently in this alternate reality the Whitehouse was destroyed on 9/11 and the twin towers are still standing.
But that doesn't quite make sense. The device Jones was using opened a window to the alternate reality at the same location. Dunham stepped off an elevator into the alternate reality. There are no buildings where the towers once stood so the window they brought her through also moved her.