The diagnostics on a car aren't quite that robust. Usually it just tells you that some sensor is reporting a bad reading - that can still be caused by countless issues (take a misfire for example, it could be caused by: bad spark plugs, bad coils, bad timing, bad fuel, bad sensors, bad cats, broken intake, broken fuel pump, etc,etc...). Does it cut down on diagnostic time? Yes. But there's still a considerable amount of diagnosis to be done in many cases. And IMO cars are a lot easier to diagnose than electronics.
With the iPhone (or any computer really), you can't really run a simple program and just deduce a part is bad. More often than not, it's a very strange combination of operations that causes the fault to be triggered. With computers for example, many of the stress testing programs won't show a fault until a few days in. But that computer may exhibit very strange behavior under normal use. Similarly with the iPhone, a diagnostics program might not catch any issues, but that wouldn't be enough to say that the phone is okay. Hypothetically speaking, if Apple found that a significant portion of refurbished iPhones end up being returned again, it might make business sense to just scrap any used phones and give new replacements. I'm not saying that's what they do... but who knows without a definitive statement from Apple.
The other thing with the iPhone refurbs is that they always recieved new screens and batteries. That basically leaves the logic board as the possibly not-new component. Identifying and replacing faulty components might cost more than the cost of the logic board itself... so it might make business sense to just stick a new one in.