Good point. For those situations, there should be a separate override button to disable the feature, just like there often is one for traction control (on normally, button lights up when disabled). Or for the passenger airbag back before weight sensors replaced a manual override.
But otherwise, even when in manual driving mode, the emergency brake feature should be active and watching for impending collisions.
That's why it should be a separate button, so that it never assumes you want to manage braking unless you specifically turn the system off. Just pressing the brake pedal doesn't mean you want automatic braking to go away.
But otherwise, even when in manual driving mode, the emergency brake feature should be active and watching for impending collisions.