Uber engineers assigned a persistent identity to iPhones with a small piece of code, a practice called “fingerprinting.” Uber could then identify an iPhone and prevent itself from being fooled even after the device was erased of its contents.

There was one problem: Fingerprinting iPhones broke Apple’s rules. Mr. Cook believed that wiping an iPhone should ensure customers that no trace of the owner’s identity remained on the device.

I expect what they do is fingerprint the device to detect fraudulent use later. Typically this is done by combining a bunch of identifiers and details on the device and then hashing the result. The output is a unique identifier for that specific device.

While technically this doesn't store any "identity" information on the device itself, if done correctly, the device could be identified and tracked across wipes (hence Cook's comment).

Of course, the article does a piss poor job explaining this, but for many readers the nuance doesn't matter... They capture the spirit well enough, even if the details are pretty misleading.

Furthermore, that code wasn't triggered, somehow, in devices near Cupertino, indicating that they were trying to hide the code from App Store reviwers.

I think I feel that this is very qualitatively different from gathering location data on users who have deleted the app (if such a thing were possible), but nevertheless a serious ethical lapse.

In my opinion Apple should have suspended their app from the iTunes App Store until they fixed the app. Because isn't that what they do to other small players? I would say there is a bit of hypocrisy on Apple's part here.