Not entirely sure what this means, maybe it's something I did wrong, but milestones seems to be preventing my headless server from actually creating a game.

   65.756 Script @__Milestones__/scripts/migrations.lua:147: Running 1.3.20 migration
   65.756 Script @__Milestones__/scripts/milestones_util.lua:391: Backfilling completion times for player
   65.837 Error ServerMultiplayerManager.cpp:84: MultiplayerManager failed: "The mod Milestones (1.4.6) caused a non-recoverable error.
 Please report this error to the mod author.
 Error while running event Milestones::on_configuration_changed
 __Milestones__/scripts/milestones_util.lua:200: bad argument #1 of 2 to 'pairs' (table expected, got userdata)
 stack traceback:
         [C]: in function 'pairs'
         __Milestones__/scripts/milestones_util.lua:200: in function <__Milestones__/scripts/milestones_util.lua:198>
         (...tail calls...)
         __Milestones__/scripts/milestones_util.lua:432: in function <__Milestones__/scripts/milestones_util.lua:420>
         (...tail calls...)
         __Milestones__/scripts/milestones_util.lua:399: in function 'backfill_completion_times'
         __Milestones__/scripts/migrations.lua:152: in function 'func'
         __flib__/migration.lua:70: in function 'run'
         __flib__/migration.lua:97: in function 'on_config_changed'
    __Milestones__/control.lua:145: in function <__Milestones__/control.lua:143>"

Sorry for the delay, I think this should be fixed now.
It was caused by migrating Milestones from a mod version older than 1.3.20.