I had originally found myself very confused by how the second order axiom of induction restricted PA to a single model, leading to this discussion where I thought doing so would violate the incompleteness theorem.
What I misunderstood is that while the axiom schema of induction effectively quantifies over properties definable in PA, the SOL version quantifies over ALL properties, including those you can't even define in PA.
This seems like a really subtle point that wasn't obvious to me from the article, knowing FOL but not SOL. I actually realized my mistake when I saw that Eliezer was representing properties as sets in the visual diagram.
Anyway, I thought others might benefit by learning from my mistake. Also, I'd like to point out that this definition of the natural numbers yields no procedure that lets you produce theorems of PA as second-order logic has no computable complete definition of provability. Just use the axiom schema of induction instead of the second order axiom of induction and you will be able to produce theorems though.
ω-inconsistency isn't exactly the same thing as being false in the standard model. Being ω-inconsistent requires both that the theory prove all the statements P(n) for standard natural numbers n, but also prove that there is an n for which P(n) fails. Therefore a theory could be ω-consistent because it fails to prove P(n), even though P(n) is true in the standard model. So even if we could check ω-consistency, we could take PA, add an axiom T, and end up with an ω-consistent theory which nonetheless is not true in the standard model.
By the way, there are some papers on models for adding random (true) axioms to PA. "Are Random Axioms Useful?" involves some fairly specific cases, but shows that in those situations, random axioms generally aren't likely to tell you anything you wanted to know.
I thought for ω-consistency to even be defined for a theory it must interpret the language of arithmetic?