This has been asked and answered many times on the forum, but no, no FSX settings are changed in your FSX.CFG, unless you explicitly use the "Save to FSX" button in the Addon Manager, which will write the settings you see there in the FSX.CFG.
However, the GSX full installer does make a SINGLE change in the FSX.CFG file, and it sets the SKINNED_ANIMATIONS parameter (which is the same as the "Advanced Animations" flag in the FSX UI), because if it was off, no animations for humans would work. This is only done by the Full GSX installer, not the Live Updates.
And, any of our Uninstallers IF (and only IF) you reply YES to the question "Do you want to remove the Addon Manager" and YES to the question "Do you want to remove the Couatl scripting engine" when Uninstalling, they will clear all the lines belonging to the bglmanx.dll and couatl.exe in the [Trusted] section of the FSX.CFG file, so the next install any trust question will be remade.
These are the only place in any of our products where the FSX.CFG file is modified, no other settings are being touched so, whatever problem you had with the FSX.CFG, it wasn't caused by GSX or any of our products.
