The System configuration scope should "affect the whole system and cannot be overridden anywhere else". The below example is OpenSSO, but I haven't found any example that works correctly.
Steps To Reproduce :
1. Find "OpenSSO" configuration in Control Panel>Configuration>System Settings (different location depending on Master or 70x). Note that OpenSSO is System Scope.
2. Enable OpenSSO. Save/Update these settings.
3. Go to Instance Settings > Authentication > OpenSSO. Disable OpenSSO. Save.
The Instance Setting should not override the System Configuration. (The box should be disabled / not toggle)
Instance setting successfully modifies this setting.
Reproduced on Master : 5536d268ebcecf0d7ef19954467146e2ec264684
Reproduced on 70x : 162ac478cac6cf08df65c7d5ac091cecd0dd41ce