The article's title simplifies matters. Technically, I'd say that science undermines theism, but that it's philosophy that explains why, so the atheistic argument itself is formulated in broader, philosophical terms.

I lay out the dilemma in the article: either God is conceived of intuitively or not. If so, the science-based argument applies since the scale of the universe is counterintuitive, meaning that scientific objectification supplies much better explanations than archaic, intuitive theology. If it's a question of appealing to the most plausible explanation of scientifically observed patters in nature, intuitive explanations give way to counterintuitive ones (because nature is much different than what the founders of the great religions thought).

If "God" is conceived of in abstract, unintuitive ways, the religion is already practically atheistic, so the science-based argument isn't needed.

I'm not saying it's impossible that consciousness or will isn't fundamental to nature. I'm saying that that appeal to intuitive categories is implausible, once we understand the humble, terrestrial functions of those intuitions. It's much more likely that we vainly project what's familiar to us onto the unknown, than that those conceptions do justice to what's beyond us in scale.