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.
The other thing I don't understand is that this paper argues against hardware timestamping on the grounds that users won't want to buy expensive hardware, and that Huygens is for "standard hardware ... in current data centers". Expensive, niche hardware is normal for the HFT folks that care about nanosecond precision.
Yes, it seems that the designers tried to make something that would work in the current Google data centers. Which is not surprising as some of the authors work at Google.
I'd more want to know: why does Google need even better synchronization of time stamps than what they have now?
Good support for PTP in network switches is rare. If the users don't want to spend a lot of money on new switches with PTP support, they can synchronize clocks in the network with a protocol which doesn't require special support in switches.
There are some interesting ideas in the Huygens paper, but I don't see anything that couldn't be done also with NTP.