Apple's justification seems counterintuitive, given that the commission only applies to app sales or in-app purchases. Since free apps don't pay anything, what is the commission for if not for "services as a payment provider"?
It's very normal for companies to charge some customers more than others based on their ability and/or willingness to pay. See: student, senior, and military discounts, SaaS with organization pricing vs individual pricing, etc.
I don't know for the US but in many countries that's just illegal if you have a monopoly.
The judge in this ruling found that Apple does not have a monopoly, so it wouldn't matter either way.