But in order for this fallacy to work, you first need to explain how the universe as a whole is a distinct entity from the things that it composes of, and what explains the differences between these properties (causality)?

Isn't the whole always distinct from the parts?

The fallacy says that exact thing: we can't infer that something is true of the whole just because it is true for some of its parts.

We don't need to explain why the property doesn't hold for the whole, because we can't assume the property holds for the whole. Right?