Re: toggling a minor mode should not tell Customize that the value has been set

[Richard Stallman]

    This means that if you so much as toggle a global minor mode, and you later
    use `customize-customized' to see which options you have edited and set, the
    minor mode variable shows up in the list of customized options.

I think this was done deliberately to make the interaction with Custom
smoother.  Otherwise Custom would say it was "changed outside of
Custom" and it would make users worry.