Portions of humanity had apparently advanced enough to understand meta-time. At least, the Time Agency did, since Jack had apparently had dealings with Time Lords and Daleks and knew they'd both been wiped out, and he, John, and Gray didn't have any problems with meeting at different points in their personal histories. River Song didn't have a command of the concept, though, since she had to use more mundane means of making sure she and the Doctor were in sync than just relying on how time travelers so rarely meet each other out of order.