If you read the link, there is a lot of conjecture there that people seem to be taking as fact.
11.2 Apps utilizing a system other than the In App Purchase API (IAP) to purchase content, functionality, or services in an app will be rejected
Apples App Store Review Guidelines
According to that long-standing rule, I assume the iFlow app was using IAP for its app's purchases. In which case, they've always been charged 30%.
If they suddenly need to avoid that 30% (it sounds like because publishers re-negotiated?), why don't they remove in-app purchasing from the app and create an online store people can go to in a browser to add to an online library (not through the app)? This is what Amazon does.
I haven't seen any confirmation that this is changing. In fact, in that linked article it says "Apple's made no change to its App Store Guidlines" and a quote from an Apple spokesperson only references apps that allow you to make purchases:
"We are now requiring that if an app offers customers the ability to purchase books outside of the app, that the same option is also available to customers from within the app with in-app purchase."
No I don't think iFlow was selling content via IAP, they (like amazon) were selling it via a web page, whether that page was linked from inside the app and popped up automatically in MobileSafari I don't know.
Either way from the agreement
"11.13 Apps can read or play approved content (magazines, newspapers, books, audio, music, video) that is sold outside of the app, for which Apple will not receive any portion of the revenues, provided that the same content is also offered in the app using IAP at the same price or less than it is offered outside the app. This applies to both purchased content and subscriptions."
That talks about any content sold outside the app. It doesn't specify how it's sold, just that it's content, it was sold and you can read/play it on the App. A strict reading of that says that if you build a pure reader with no IAP, not even a handy button which links you to mobilesafari to take you to a webpage to buy content, you still have to add IAP to your app and allow the same content to be purchased at the same price in the app.
To reduce it to absurdity, if your model was to keep content on a server and access it via an app and the only way you could add content was to go down to your local 7-11 and hand over money and they secretly upload the content to the server, no web store, nothing, you still have to make that content available via IAP.
This - to my personal reading - means that Amazon's Kindle app falls foul of the rule. You can access content which you purchase outside (via amazon's website) so it must provide IAP for the same content at the same price. Just removing the 'link to amazon website' is not enough.
As I say, that's my interpretation of those rules from reading them.