https://drive.google.com/file/d/1ax0pxJtkIeJIJR-yqpG-3wzs94AO4lPO/view?usp=sharing
The desync report is shared using the above link.
So in multiplayer, when someone connect the Subzero Phase Array Beacon(SPAB) to liquid nitrogen using pipes, everyone will desync. Already connected SPAB won't cause this problem but disconnect the pipe from a connected SPAB will immediate desync everyone.

Not sure exactly why, but the issue arises from the Afraid of the Dark mod—desync doesn't happen with it disabled.

E: This was incorrect.

Updated to 1.2.16, Turned off Afraid of the Dark, started a new map, entered cheat mode with Editor Extension and tested again, still desync.
Desync log: https://drive.google.com/file/d/1QdHbfVivsS0uGQQpdCDfT-g1_bc-B50-/view?usp=sharing

On this end using /toggle-heavy-mode no crc error doing any actions with SPAB.
Check what happens on that end with /toggle-heavy-mode in chat and then performing desync action.

The following message is printed the moment desync happened.

Heavy mode check after-scenario-update-19795 failed
Heavy mode heuristic check after-scenario-update-19795 failed

Any log file you would like me to upload?

Well not sure if these are useful, I'm uploading my dumps(I'm the host) and my friend's desync log
https://drive.google.com/file/d/1nWhOKdpD2Ybno_tFfpoaJnlovAobH2xo/view?usp=sharing

Desync is fixed in 1.2.20. Thanks.

Never mind it still desyncs, just less frequently and sometimes not everyone desync...

Will go through the powered beacon code next.

There appear to be two desyncs.

One occurs placing powered beacons—the why is not yet isolated.

The other occurs during Liquid nitrogen/oxygen -> Nitrogen/Oxygen gas conversion which occurs if the Liquid variants are in non-insulated pipes.

In factorio 2.0.43 changelog: "Fixed that setting fluids on a FluidBox via Lua would give fluids to ghost entities, which would cause a consistency check failure"

Not entirely sure that in particular is fixed?
Maybe related to removing and setting fluid within same tick?

Continuing investigation.

Fix in 1.2.21.

It's not causing desync now. Thanks. However, it now causes a fatal error:

The mod Nonstandard Beacons (1.3.4) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event zzz-nonstandard-beacons::nsb-beacon-rotate (ID 226)
zzz-nonstandard-beacons/control.lua:394: attempt to index field '?' (a nil value)
stack traceback:
zzz-nonstandard-beacons/control.lua:394: in function <zzz-nonstandard-beacons/control.lua:385>

This happens when any player try to rotate a SPAB in multiplayer, even just the ghost.

Recommend not rotating SPAB until NSB library is updated.

e: Also recommend deleting previously placed SPABs in version prior to 1.2.21, also pending NSB library update.

Solved in NSB 1.3.5.