What instruction the addon manager saved in FSX configuration?
Nothing, if you changed only the Anti popup and the other settings you see in the box labeled "Addon Manager Tweaks - applied only to sceneries handled by the Addon Manager", because these settings are saved in our CouatlAddons.INI file under %APPDATA%\Virtuali.
The other tweaks, labeled "Sim Tweaks - applied globally for all sceneries", will be saved in the FSX.CFG, but only after you explicitly enabled them first and then pressed Save. Nothing in the FSX.CFG is changed automatically, unless you said so.