I maintain an NTP implementation. That comparison doesn't seem fair to me. It looks like they are comparing the old reference NTP implementation and not really the protocol itself. An NTP implementation can certainly synchronize clocks with better accuracy than 1 millisecond, or even 1 microsecond with hardware timestamping and good network switches.

There are some interesting ideas in the Huygens paper, but I don't see anything that couldn't be done also with NTP.