I highly doubt the submission terms contradict the App Store terms. Or do you have a source which shows that the submission terms state that 3rd party licenses are not accepted (and therefore apps based on GPLv2 source cannot be distributed)?
It's a pass through clause.
GPLv2 would only be prohibited from distribution via the App Store if the App Store terms did not include the ability for a submitter's GPLv2 to supersede the App Store license.
3rd party licenses are acceptable if they're compatible with Apple's terms.
Does the GPL attempt to force Apple to do anything, like distribute app source code, or distribute an app without DRM? If so it isn't compatible.
It's very simple. You're not supposed to submit an app that makes Apple legally liable to fulfill the requirements of a license. You, the submitter, have to fulfill all the license's requirements yourself, without Apple being involved.
If your app uses something with a license fee, you have to pay it, you can't have the licensor bill Apple for it. If there's a contract with a rights holder, you have to sign it, Apple doesn't sign the contract.
The app has to be unencumbered and safe for Apple to distribute via the App Store, with the App Store's policies and methods. If the license requires action on Apple's part to be in compliance, You Shouldn't Submit The App because it's not compatible with the App Store.
(Examples of "license requires action on Apple's part":
1. If Apple would be required by your app's licensing to distribute the app without DRM, it's not compatible with the App Store. DRM was part of the deal. App submitters know that going in.
2. If Apple would be required by your app's licensing to distribute the app's source code, it's not compatible with the App Store. Apple-distributed source is not part of the deal. App submitters know that going in.)
I assume the 3rd party licenses the end-user agreement is mostly talking about are things like content licenses, like art and other media in movie tie-in games. Or books downloaded into the kindle app.
A kindle book is probably licensed from the author to the publisher, and the publisher to Amazon for distribution rights, and from Amazon to the end user who buys it. That's a lot of 3rd party licenses, that are compatible with the App Store.
It's a pass through clause.
GPLv2 would only be prohibited from distribution via the App Store if the App Store terms did not include the ability for a submitter's GPLv2 to supersede the App Store license.