i unchecked the underground attacks setting in the mod menu and still had biters digging their way out of the ocean making tiny islands to stand on as they shot at my helicoptor

The error is not reproducible. I need your save where the underground attack is visible and the setting is disabled

Same error here, after disabling the setting and saving the underground attacks persist and the settings come back to enabled.

Perhaps one of your mods is blocking the settings. Also, if this is a game on a server, you may not have the rights to change the settings
I recommend checking in your local game (in new game, do not load this save). Leave only Rampant Fixed from the mods. Try changing the setting and check if it is saved. It works for me.
If after checking you still can't save the changes - send me the save

I changed the settings directly in the mod file and it solved my problem for now

I changed the settings directly in the mod file and it solved my problem for now