Or, in a sentence: you can't claim something is indivisible, and then charge for its pieces separately and at separate times.
Your point is probably that developers and customers are two separate groups, and there's a history of making a thing free to customers (the App Store) while charging vendors (developers) for the privilege.
I just don't see how your "then" follows from your "if" at all! The integration of iOS and the App Store is from a user's perspective. No one seriously believes that Apple is claiming that the two things are literally physically impossible to split up technically. You might as well be arguing that it boggles the mind for the calculator app to be free, but for iCloud storage to cost money!
Except Apple in the court does. That is the exact stance why they cannot allow third party stores and browser engines since those are technically a part of indivisible OS services. Of course, this is obviously BS and inconsistent to many other Apple's business practice, anyway it's their official legal stance in nearly all of its antitrust lawsuits.