SuperSU does not grant root during boot
The app (affect 3C Toolbox, System Tuner) may not be granted root during boot, hence fail to apply any boot settings!
This is caused by an option in SuperSU which is disabled by default "Enable su during boot". Simply enable it and everything will be fine.
This option when disabled will refuse root to any apps (even though root has been previously granted) until SuperSU receives the BOOT_COMPLETED message from Android. This makes the whole process very unreliable because there's no way to predict when apps will receive the BOOT_COMPLETED. This message is sent to all apps (having requested it), one after the other. So any apps receiving the message before SuperSU will not be granted root. Any apps receiving it after will be granted root.
Please also note that this option is very misleading into making us believe all apps will receive root, even those which did not get manually granted root. This is not true, only apps manually granted root before will receive root during boot.
In summary the SuperSU option called 'Enable su during boot' must be enabled in order for any boot settings to be applied properly and this is true for any apps on Play Store using root during the boot process. Sadly this option has been turned off by default and may cause any root apps to dysfunction dramatically.