The patched core brightness you made did the same to my MacBook 15 2010, once I replaced the original one back, the keyboard/trackpad settings functions normally again.
You could be right, because that CoreBrightness was patched from a Mojave beta 2 clean installation its original size was 640 KB, and after patched became 648 KB.
While instead I've double checked now from Mojave beta 4 that file size is 718 KB.
If this is right, it means that Corebrightness needs to be patched on every Mojave beta release, the older one even if enable Night Shift correctly maybe produces the unwanted effect you described.
I will give an attempt in a while and let you know, meanwhile thanks.
edit:
Unbelievable, that was exactly the cause of the issue, Thank you very much!!!
Anyway I will try to recreate the Corebrightness Patched from a clean Mojave beta 4.
I need more time it seems the new Corebrightness.framework has changed.
edit2:
I see you joined today and fixed this important issue, you should attend the forum more, your debugging skills have been impressive!
Not only because you fixed my issue but you have discovered a correlation between "System Preferences" (in particular affecting those three prefpanes) with the CoreBrightness PrivateFramework.
edit3:
Just to exculpate myself, I followed correctly the pikeralpha's method in my binary patching, infact I have trying also replacing the untouched CoreBrightness from Mojave beta 2 putting into Mojave beta 4 and the same prefpane issues occurred again. So my manual patch worked fine until Mojave beta 2.
I guess after Mojave beta 3 release Apple has changed in Corebrightness.framework something major.