Thank you all for your advice.
After several days of tinkering, I got several things modded. There are still quite a few things left to do.
This is what I did by editing base.charscript, and it worked fine.
I don't know offhand but might be able to help you find it, where did you find Obedient to mod?
In Potions.txt. I can use the extractor now, but I'm still not able to find the place to edit the other traits bonuses.
... because they are hardcoded in the .exe as said above. So the place is EoCApp.exe.
You can query the scores of a trait in Osiris, but the effects are hardcoded.
It is hardcoded that the Obedient trait makes a player use the potion 'SKILLBOOST_Leadership1_Obedient' instead of the potion 'SKILLBOOST_Leadership1' when the character sees a party member with Leadership 1. All other traits don't use potions but their effects are directly applied. The fact that a potion is used makes Obedient changeable but not the other traits.
As said, you can monitor the traits in Osiris and catch the events when they are changed, but you cannot modify the traits and their effects directly. (You could not even modify the effect of the trait Obedient, which is using a specific potion, you could only modify the potion itself.)