If I use an Apple device then I am clearly using an Apple product and I have a relationship with Apple.
If I use an application then I am clearly using their product and I have a relationship with the application developers.
If that application embeds third-party tracking, I am not clearly doing anything with the third party and I don’t have a relationship with that third party. Therefore Apple requires that the application developers ask for my consent first.
Only one of these needs the user’s consent, and it’s clear why. Apple can act fairly and still hold third-party tracking to a different standard.
But that argument is not limited to tracking, isn't it. For example if I use an application that integrates with Shopify or Stripe, by that logic Apple would also be in the right to ask for consent (while the integration with Apple Pay would be pop-up free). In fact I don't see any reason why Apple shouldn't go after those businesses next - there's a clear privacy angle they can play here too. As much as I like Apple Pay as a consumer, I don't think Apple should get a blanket pass on favoring its own infrastructure over any third-party integrations just because the user is less confused about their relationship with Apple.
On the other hand, third-party tracking is not silently disabled either - instead, it prompts the user on first run and the user is given the choice to opt in or out per-app.
Gee, I wonder why...