The Article states to see the use of them, but then fails to do so itself or even speculate on how they would be used given the scenario Mr. Terrific is encountering.
I'm not entirely sure I understand your meaning here.
The author does not even attempt a skeptical analysis of the dieties in question and simply assumes that All Myths Are True even though they are extremely contradictory especially in regards to origin stories and throwing into the fact that many of the laws of physics and nature operate in roughly similar ways to the ones that exist in the real world.
The thing is, in the context of the DCU, those myths, gods and aliens and magic, they are true. Mr Terrific can't go around saying "you know you're not really flying, Superman, it's an optical illusion/it's all in your head." Superman is flying. But in the DCU there is a scientific explanation for it, and there could just as easily be scientific explanations for Zeus and Gog and the Spectre. It'll be Comic Book Science that wouldn't fully pass muster in the real world, but it would still be able to debunk the so-called fact that there are deities within that fictional universe.
The author is extending Mr Terrific's logic that what makes a god a god is how we view them. I mean, I could argue that God exists simply because the life of a person who believes in Him is affected by that belief, and if something can affect something or someone else, then it is real in some way or another, even if it isn't really real. My arguing that point does not conflict with my atheism in the slightest because it's all about perception. If someone else believes that God is real, then that is real for them. If someone in the DCU thinks that Superman is a heavenly angel, then that logic probably works for them, and as such it's true, even if other people would react with "LOLwhat, he's Kryptonian, dude."
Of course it's always possible to use scientific analysis to provide evidence as to why so-and-so isn't a god or why such-and-such isn't a mysterious form of magic. But for every person, the truth is relative. Two people can be looking at the exact same thing and they may interpret what their senses tell them completely differently from each other.