First, I didn't suggest that Apple can collect the same commissions outside the app store. Indeed, I've suggested at various times that Apple might need to reduce its commission somewhat for sales made outside an app (or the App Store). That would be to mitigate the risk that future plaintiffs could make an antitrust case based on illegal tying (to the use of the App Store or Apple's IAP). As we now know that's what Apple has done; it reduced the commission by 3 percentage points to reflect the cost of payment processing. Further, Apple certainly shouldn't increase the commission for sales made through other parties. That would make a potential antitrust tying case stronger.
That said, the best citation would be the ruling which I referred to. I encourage people to read it (among other court documents), in its entirety, if they want to understand for themselves what it actually says and what it means for Apple going forward. It discusses Apple's right to collect commissions multiple times. Because of how antitrust law works - looking for anti-competitive effects, then considering pro-competitive justifications, then considering possible alternate means - Apple's legitimate business interest in being compensated for the use of its IP is relevant to the case.
So I'm not going to quote every part of
Judge Rogers' Rule 52 order which refers to this issue. Again, people can read the opinion for themselves if they want a fuller sense of what it means (and want to be in better positions to discuss various issues related to it). But in response to your doubts, I'd point to this one specific passage and corresponding footnote:
I'd also note that the court was aware of the terms of Apple's developer agreements. The opinion discusses some of them, to include the commission requirement. Then it issued the injunction stating what Apple couldn't do. That injunction says nothing about Apple no longer being able to enforce the terms of its developer agreements which require the paying of commissions. If the court meant to prevent Apple from continuing to require commissions be paid, the injunction would have said as much. Of all the contractual terms considered in the case, the court only prohibited what it prohibited - the so-called anti-steering policies.
What will happen now is plaintiffs (e.g. Epic) will challenge the
amount of the commissions Apple requires for payments made through other parties. And that's where Apple will present evidence and make arguments as to what is reasonable compensation for, perhaps among other things, the use of its IP. The irony is that, the more the commission requirement (which Apple has an indisputable right to based on its legal monopoly on its own IP) is un-tied from other requirements (e.g. that developers use IAP or distribute apps through the App Store), the less Apple needs to justify the amount of that commission. It's only because of the tying that the amount of the commission is somewhat challengeable.