That’s possibly either a PTR thing or something specific to particular graphics cards. As I’ve just checked via Console mode and can confirm all options are on by default (except gxMTDisable of course)
They get removed as that’s not how the gXMT CVars operate.
AKA their settings do not get saved. When you open your game all multithreaded options are on by default. You get individually turn some of them off but their settings will not save anywhere and they will all be on when you next open your game.
The best way of checking if they are on or not is via Console mode :