The Borders app was basically a rebranded version of the reading app developed by Kobo, which raises an interesting point. Kobo haven't updated their app yet, and their app still has the ebookstore physically inside the app. I've been told that they think they're immune (possibly because they're a Canadian company), and I'm beginning to wonder if they do believe that.
There is 1 detail about this app that surprised me. Borders will still let you create an account from inside the app. That's odd, because last week I followed a series of tweets from one developer about this very issue, and he had a different outcome. Apple wouldn't let him build starting an account into the app. Apple won't even let him link to the website so users can create an account there.
On the other hand, Apple have been notably capricious in the past about who has to follow which rules. For the longest time now I've had the feeling that enforcement was largely dependent on the whim of whichever Apple flunky was involved at the time.
Today's news tends to support that hypothesis.