I noticed that when I change worlds, the waypoints stay the same. For someone with many worlds, switching between waypoint groups manually could be confusing / annoying. Perhaps it would be possible to make waypoints world-specific?

Seems to be a bug. The waypoints are world-specific, but if you open one world, exit (and don't quit Minecraft), and open another world, the mod keeps saving waypoints to and loading waypoints from the file for the first world's waypoints.