The latter generally works for sum type states.

It's not when desirability of fnurbification negatively correlates to other items, i.e. when following is normal config:

  [X] perform deconbinaturation 
  [X] disable fnurbification 
  [X] enable entrapollation

... in this case there is a reason to make it a "positive-disable".

Nope, just mark which config is default and add tooltip explaining to user why it might need to be changed.

Aiming for all options to be "on" or "off" is some pedantic nightmare that makes settings harder to navigate

> Aiming for all options to be "on" or "off" is some pedantic nightmare that makes settings harder to navigate

This probably stems from config files or in-app defaults where a feature is default-on and so the existence of a value means something is disabled. And then some dev comes along and mindlessly transcribes a bunch of boolean flags into a settings menu and here we are.