I'm pretty sure they are only interested in books purchased on the device. If you don't purchase it on the device they don't get a cut.

AFAICT, the article is saying that if there's a way to purchase content externally and move it onto the device, there must also be a way to purchase it internally with the AppleVAT.

So they're definitely targeting books purchased off device.

Let's hope so, but the article put it differently - if an app presents content bought elsewhere, there must be an option to buy that content also in-app. So if you are right, the article is wrong.

That's isn't to say that they won't try to find a way. :)

They likely won't.

There are also plenty of PDF readers in the store already (Goodreader, for example) that are independent of Apple's iBooks.

Unlike Sony, Apple isn't generally known for removing functionality from products after purchase...

But they are well known for pulling apps arbitrarily, so make sure you download and install as many book readers and other apps with similar type functionality now. For instance, I'm glad I installed the Safari Online reader when it came out. (Although in this case it was O'Reilly that pulled it due to whiny complaints that it wasn't a native app).