You're right and this has been glossed over by much of the commentary in this thread. If you read the ruling the judge repeatedly stated that Apple is entitled to compensation for its intellectual property, regardless of whether that is achieved through IAP or some other means:
> Under all models, Apple would be entitled to a commission or licensing fee, even if IAP was optional.
> Turning to the intellectual property justification, the Court agrees with the general proposition that Apple is entitled to be paid for its intellectual property.
> As established in the prior sections, see supra Facts §§ II.C., V.A.2.b., V.B.2.c., Apple is entitled to license its intellectual property for a fee, and to further guard against the uncompensated use of its intellectual property.
> The Court also notes that in the but-for world where developers could use an alternative processor, Apple would still be contractually entitled to its commission on any purchase made within apps distributed on the App Store.
In other words, even if developers are allowed to link to alternative payment processors inside their app, Apple may very well still be entitled to some sort of commission/licensing fee for the use of their IP.