Why doesn't Bethini affect the second SKyrimPrefs.ini folder?

[4mericanRogue]

Hi, I used Bethini for the first time and it worked pretty well but what concerned me is how skyrim special edition has two different locations for the ini files. Documents/mygames/skyrimspecialedition is the folder where the defualy ini files that bethini alters are but the second skyrimprefs.ini file in the actual game folder installed by steam doesnt get affected by bethini and that concerns me cause i dont want file conflicts and or the bethini tweaks not eve working becaus eof that.

[DoubleYou]

This is intended behavior. The INI files located in the game folder are not used by the game. Instead, they are used by the launcher to create the initial ini files. 

[piranha45]

How would Bethini interact if I edit the skyrim.ini & skyrimprefs.ini files through Mo2?

Bethini offers a couple ini edits, yet many are not available...  So to change them I'd have to go through mo2.  But will that cause conflict with what I've changed in Bethini?

[DoubleYou]

You can make custom edits in the Custom tab. It is also fine to use the MO2 ini editor.