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

[Richard Stallman]

    Fair enough. Would you then change all commands that change option values so
    that they too tell Customize that the value has been customized? Would you
    somehow make sure that not only commands but all Lisp code does the same
    thing?

That approach (all or none) is basically mistaken.

Anyway, there's no point spending more time discussing this; I've told
you the decision.