This specific example definitely feels like an abuse of the patent system. However, the rest of this article relies on weak connections and examples from other industries to argue that medical patents must die. If medical patents die, medical innovation dies.
For a moment, let's apply the realities of "medical innovation" (researchers across private and public fields) to internet innovation. Imagine that every app you published took four years and $100M to get to a testable product. Keep in mind, this is still unusable. You go out and spend millions more testing it on "fake users" (animals). If this works, you need to go raise hundreds of millions more to test it on your first batch of real users... then a second... then a third.
Billions of dollars later, you realize that your app doesn't work as it was intended. You've just spent 6 years and billions of dollars figuring that out. There is no fail fast, in this world.
Lets say your product actually makes it to market. Congrats, now you need to compete against copy cat app developers who can replicate your app at a fraction of the price. How do you defend yourself? Innovative marketing? Large email list? Good SEO? SEM? None of that works in medicine, because the switching costs are positive for a patient.
This is why we need patents. Without them we would see a significant reduction in medical innovation. When markets don't create enough risk-adjusted incentives to promote innovation, the government must step in to create those incentives. I'm not saying our system is perfect, but it's better than nothing (at least in medicine).
I spent a long time working on a medical startup and it's orders of magnitude more complex than most of the apps we see celebrated in our hacker community. I would bet that the typical FDA application is longer than the entire printed code base of most web apps.