How to reproduce desync:
Join game, unpause if it was paused, wait some time, rejoin again self (better with reloading game) (not always leads to desync), or, let your friend join (100% chance of desync).
How we avoid this desync:
Relaunching server completely, joining both on pause state.

We thought it's some other mod, but today I decided to check desync report, I have no idea what does it mean, but here is difference in: latest_input_actions, level-heuristic, level.dat0, level_with_tags and script.dat, I checked all different files, and have no idea what it is inside of them, beside it's some hex thing, but, in level-heuristic I noticed some difference in values between something with random tag on it, and in script.dat I noticed a lot of things related to biters and rampant, like mutation, squads, etc.

desync report zip: https://drive.google.com/file/d/1vLx86ekJxzt8rVjFBKhJ3qI2JWtENnjK/view?usp=sharing

mods used:
2.601 Script @aai-loaders/data.lua:5: Log mods once: {
BigElectricPoleRange = "1.0.1",
BottleneckLite = "1.3.4",
CleanFloor = "2.0.0",
EasyQuality_Ham5_fork = "0.0.1",
EditorExtensions = "2.5.2",
Fill4Me = "0.12.1",
["Flare Stack"] = "4.1.0",
GUI_Unifyer = "2.0.1",
HeroTurretRedux = "1.0.35",
KetsRadars = "2.0.1",
ModuleInserterSimplified = "2.1.1",
["Nearby-Ammo-Count"] = "2.0.1",
["PipeVisualizer-Updated"] = "2.4.4",
RailTester = "0.9.5",
RampantArsenalFork = "1.0.4",
RampantFixed = "2.2.4",
RateCalculator = "3.3.8",
Repair_Turret = "2.0.4",
ResourceEraser = "1.0.0",
Smart_Inserters = "2.0.20",
SpidertronEnhancements = "1.10.8",
StatsGui = "1.6.1",
SteeperQuality = "1.0.2",
Tapeline = "3.0.4",
TimeTools = "3.0.8",
["Todo-List"] = "19.14.1",
ViidisElectricOffshorePump = "2.0.2",
WideChests = "6.2.4",
WireShortcutX = "1.3.1",
["aai-containers"] = "0.3.2",
["aai-loaders"] = "0.2.11",
["aai-signal-transmission"] = "0.5.3",
["ammo-loader"] = "2.0.5",
assemblyanalyst = "2.0.6",
["automatic-underground-pipe-connectors"] = "2.0.11",
base = "2.0.73",
["belt-balancer-3-1"] = "1.0.2",
["belt-visualizer"] = "2.0.2",
["bottleneck-analyzer"] = "0.3.7",
["chest-auto-sort"] = "1.3.0",
circuit_visualizer = "2.0.2",
compaktcircuit = "2.0.26",
["crafting-queue-enhancements"] = "0.0.6",
["dqol-resource-monitor"] = "1.5.9",
["elevated-pipes"] = "1.4.7",
["elevated-rails"] = "2.0.73",
["even-distribution"] = "2.0.2",
["factorio2-thomas-the-tank-engine"] = "0.3.2",
factoryplanner = "2.0.44",
flib = "0.16.5",
["flow-config"] = "2.1.6",
helmod = "2.2.12",
infinite_worker_robot_capacity_research = "2.0.2",
["inventory-repair"] = "20.0.3",
jetpack = "0.4.16",
["lane-balancers"] = "1.2.2",
["logistics-insights"] = "1.0.10",
["mining-patch-planner"] = "1.7.16",
["more-landing-pads"] = "0.0.1",
pipe_plus = "0.2.1",
["pollution-scaling"] = "1.0.7",
pump = "2.1.20",
qol_research = "3.4.2",
quality = "2.0.73",
["quality-down-binning"] = "0.5.0",
rampart_heavy_wall = "0.2.2",
["roboport-charging-pads-count-quality"] = "0.0.2",
scattergun_turret = "8.0.9",
["signal-display"] = "1.5.3",
["small-nightvision"] = "1.0.0",
["some-autoresearch"] = "2.0.7",
["space-age"] = "2.0.73",
["squeak-through-2"] = "0.1.4",
yafla = "0.1.16"
}