The article doesn't get very concrete, and given the origins of "'pataphysics" as parody I'm not sure how seriously to take this.
On the other hand, treating software systems as realities in their own right – with only incidental mappings back to our reality – is a fascinating idea. (Obviously an entirely self-contained reality is no good; I/O are pretty fundamental.) I guess the question is, what happens when we stop requiring software model things, and instead let it be things?