One point worth mentioning.
Johnson's equation of metaphysical and methodological naturalism implicitly assumes scientism - in the form of the view that science can successfully investigate anything that exists. Most scientists would not agree (and therefore even if they were "wrong", Johnson's argument does not apply to them). Johnson has yet to demonstrate the truth of this assumption, or even produce a strong argument for it.
I would further note that Johnson's claim amounts to the assertion that there is (or at least can be) a successful evidential apologetic, which contradicts the Presuppositionalist view.