Atrocities I made a similar facility as you did and tested it. I does not work because the ability "Change Bad Intelligence Chance - System" is not functional. The same is true for this aspect of the fate shrine.
Sorry.
I sincerely hope that Aaron does do one more patch for SeIV and fixes this ability.
__________________
Creator of the Star Trek Mod - AST Mod - 78 Ship Sets - Conquest Mod - Atrocities Star Wars Mod - Galaxy Reborn Mod - and Subterfuge Mod.
The lower bad intel event chance does not work well. What I think it does is make the system the facility is in less likely do be chosen randomly when you do a mission with a random target. It certainly has 0 effect on targeted missions against objects in that system (of any sort). That I have tested.