SYMPTOM
Assigning privileges "By pass all security access checks", "configure governing" and "configure caches" to a user, then this user is able to access Project Configuration editor and configure governing/cache settings as shown below:


Assigning the same privileges to a Security Role, add a user to this Security Role and select this Security Role for the project, but Project Configuration option is disable for this user as shown below:

So this user is not able to configure project governing and cache settings.
CAUSE
This is working as designed. When applied at the user level, privileges apply to ALL projects and the configuration. When applied via a Security Role, they only apply at the project level.