Apple doesn't own any rights to the VLC application being distributed. I thus see no legal basis for them to impose any restrictions, try as they might.
That clause in the GPL seems intended to cover distribution of a derived work, where the distributor owns the rights to additions they have made.
My understanding was that to publish to the app store, the publishing developer must agree to certain GPL-incompatible terms and restrictions. Apple seems to think that their terms have been fulfilled but FSF has said that GPL and App Store terms seem to conflict. I think Apple is in the clear wrt GPL but the publishing developer may have violated its terms.
That clause in the GPL seems intended to cover distribution of a derived work, where the distributor owns the rights to additions they have made.
Edit: IANAL