My summary: humans are irrational in the axiomatic sense partly because they are rational. All three of the identified "failure" modes reflect forms of rationality that humans are especially, if not uniquely, adept at.
Now that I've read the paper, I think Stanovich agrees, or in other words, I have just agreed with him.
New paper from Keith Stanovich (one of my favorite cognitive scientists):
Several formal analyses in decision theory have shown that if people’s preferences follow certain logical patterns (the so-called axioms of rational choice) then they are behaving as if they are maximising utility. However, numerous studies in the decision-making literature have indicated that humans often violate the axioms of rational choice. Additionally, studies of nonhuman animals indicate that they are largely rational in an axiomatic sense. It is important to understand why the finding that humans are less rational than other animals is not paradoxical. This paper discusses three reasons why the principles of rational choice are actually easier to follow when the cognitive architecture of the organism is simpler: contextual complexity, symbolic complexity, and the strong evaluator struggle.
Enjoy.