Some ini's do revert to default unless you set them as Read only in the file properties (eg baseengine.ini).
The reason you can't use these keys in the remap menu is because the functions they are associated with cannot be remapped (x-weapons radial, c-skill radial, z-gadget radial)
There might be a couple of other, but basically if you see a control listed in the instruction manual but not on the keymapping screen, the key is locked out for remapping.
Also, while you can remap the use function away from the spacebar, I found that during the hacking minigame my new use key would not set the "left" code. Once I switched back to spacebar I could complete the hacking game just fine.