If that is sth. that FW wanted to fix, the less intrusive change would be for the BIOS to not overwrite that value whenever it boots, but as long as the EC’s battery backup remained powered (i.e. the EC remembered what was last configured), just leave those settings be.
Technically, the non-volatile BIOS settings should only be needed to restore settings after the EC was completely unpowered (like after removing the battery. both, if the system has the backup battery). Would require much less interactions between different systems. Potentially with a BIOS setting to always force override all settings the EC can persist across reboots (keyboard backlight brightness on FW13 is for example also one of those).