The ruling also discusses and recognizes Apple's right to collect commissions on sales even when those sales take place outside the app and through alternate payment mechanisms. Indeed, this is one of several reasons why Apple prevailed on all the antitrust claims. It has a legitimate, pro-competitive, interest in collecting such commissions.The ruling explicitly states that third parties can direct their app users to other payment mechanisms, outside the app store, which avoids the app tax. So I can provide a free app, and then direct users to pay for additional app content by telling them to go to my website. This is a big deal, which is why Apple was spending millions to fight it.
Judge Rogers' opinion makes it clear that Apple can continue to collect commissions for, among other things, the use of its IP - even when payments are made through other parties - and it can facilitate such commissions through contracts (i.e. developer agreements) and, e.g., audit requirements. It will require a little more effort because of this injunction, but Apple can still do so.