Besides a simple "It's Apple's App Store and they'll do as they want to"...
Netflix does not provide any registration mechanism within the app. When you download the app, the first thing you get is a login screen (and a Forgot Password link). Nothing else is present.
Spotify has a registration mechanism in the app, but it also allows you to purchase subscriptions within the app. Rdio uses the same method. (As an aside, Rdio charges more for the in-app subscription than it does if you use their website to subscribe, to account for the 30% cut that Apple takes. This is allowed.)
Basically the answer is, you can provide a registration mechanism in the app, but you must also set up IAP for your paid subscription. Otherwise, you can provide a login screen for your customers who have subscribed outside of the app, but no links to your registration or subscription websites.
Look at the Review Guidelines section 11.14 (emphasis mine):
Apps can read or play approved content (specifically magazines, newspapers, books, audio, music, video and cloud storage) that is subscribed to or purchased outside of the App, as long as there is no button or external link in the App to purchase the approved content. Apple will only receive a portion of revenues for content purchased inside the App
Amazon and eBay are not using In-App Purchases (IAP) to purchase their products. For instance, I have an app that allows an IAP for users to access other features of the app. The purchases are made in the app for something that is part of the app and the users are able to pay via iTunes/AppStore payment process.
Amazon and eBay allow you to make purchases thru their apps but they're not done for things like 'no advertising' or 'add social media access'. They're for goods and services that are not being made thru the Apple-provided buying medium, iTunes or the App Store. So these purchases are not IAP purchases.
Best Answer
There have been several cases of people blogging about review guidelines, and AFAIK, nowhere does Apple ask us to agree to an NDA about the guidelines when creating our developer account (at least, they didn't for me).
Here's a few cases of the guidelines being blogged about:
iClarified, LocalMediaInsider, ReadWrite, engadget