<Snipped quote by Caldizar>
Which is why the scheme of clusters exists. I don't see why it doesn't reasonably fit within the standard model.
Because a Living God is, again, beyond that by their very being. I mean reading through the CYOA itself and the lore it's author made on the structure of the Verse should make this quite apparent. The only times in which it seemingly differs is when you have a Master God in charge of a Verse, in which case I assume the Living God is equal in power, thus resulting in a stalemate. But Anarchic builds don't have those since they prioritize player interaction.
And yes, it is illogical to assume that because a Living God exists Existence would have been erased. If we assume it's literally just Zachary, well the question then becomes why would he destroy Existence? He's done nothing but avoid having to use his powers, and even in the times he does I've not envisioned them being massively destructive changes. The only large-scale manipulation I have in mind, as a matter of fact, was that he used that Subtle ability to erase all traces of his existence from his home Verse.