The only check when the achievement is granted is completion of the Betrayal quest which seems to complete unconditionally after the game flips the world and does some housekeeping (failing/removing some side quests). This quest is also the only place where the achievement is referenced.
The whole evidence thing is a different quest that is active long after the Betrayal quest completes, spans multiple locations across the entire map and affects whether you can clear A.I.M. from the accusations.
Completion rates can be misleading. Take the Tactician achievement, controlling 50 sectors. By the time the world flip happens most players will have gotten this (unless you do Time is Money, Lone Wolf) yet Steam shows only 35% compared to the 25% for Saw it coming. Another example: In Ori and the Will of Wisps (over 2 years old, very popular) 40% never got the achievement for making it to a central early game area.
Makes sense, either I am missing something obvious or it is bugged.
If any of you are curious about poking around in the game files for yourself:
Use https://github.com/nickelc/hpk to extract the hpk archives (Data & Lua mostly). Some of the lua files are in a binary intermediary format for which you need https://github.com/HansWessels/unluac. There is a mod on nexus with all the necessary tools: https://www.nexusmods.com/jaggedalliance3/mods/38?tab=posts where you basically just run the .bat file (if you get an error you might have download the .NET 6.0 runtime https://dotnet.microsoft.com/en-us/download/dotnet/6.0)
Two relevant files are Data\Achievement.lua (search for "SawItComing") and Data\QuestsDef\04_Betrayal.lua (search for "TCE_ResolveQuest" and work your way backwards). It is all very declarative and fairly straight forward, but having a decent text editor with syntax highlighting and code folding (sublime, notepad++, ...) will make navigation easier.