The problem with your whole post is that you are putting in a source that's not needed.
For simplicity I'm going to reduce your argument to something silly so that you can more easily distill what I am saying.
Athetists believe that cookies come from cookie dough and that they are made in the oven.
Fundamentalists believe that cookies come from cookie dough but that they are imbued with magical cookie goodness from God while they are in the oven.
Further, Fundamentalists claim that Atheists can't disprove that God imbues cookies with magical goodness regardless of their believe or disbelief in him.
You are correct, we can't disprove God's magical goodness that he imbues in cookies. But that doesn't make the act real.
Just because you have a cookbook from two thousand years ago that says "God imbues cookies" doesn't make it so.
If you want to buy into the "God does magic stuff without us knowing it" thing, that's fine. But you can't just pick and choose where God does his magical stuff.
God makes homosexuals through his magic gay-a-fying ray gun.
God causes priests to perform acts of child abuse because that is pleasing to him.
God causes all cancers which strike down young children, because God hates children.
You can't disprove any of those statements, therefore they must be true.