It wasn't my idea so, no, that was never my plan :)

Though, you do raise a valid point, so let's see how it plays out.

    setTimeout = function(){...}
    delete setTimeout  // true - you've removed the patch

    window.setTimeout = function(){...}
    delete window.setTimeout  // true - you've removed the patch

    window.constructor.prototype.setTimeout = function(){...}
    delete window.constructor.prototype.setTimeout  // false - the patch is still there!

I don't know about the hierarchy of the prototype chain up at this level but it seems to work.

Maybe there's some other way of getting to the built-in setTimeout so you can create your own version to mask the one I added?

EDIT you can embed an iframe and rip the native setTimeout from there.