However, there is a distortion in your post that is very, very critical for this argument.
Like all software licenses, the GPL controls DISTRIBUTION of the software. This is a legal concept, not a technical one. Downloading software to your computer and copying it to your iPhone isn't distribution, because you own both devices.
The GPL, as a copyleft license, specifies that a distributor may not make any additional restrictions on future distributors (like users). This is so I can't redistribute Linux as proprietary software, for example.
However, Apple had, at the time of the VLC removal (and likely has similar wording today), this clause in the App store ToS:
>You acknowledge that Products contain security technology that limits your usage of Products to the following applicable Usage Rules, and, whether or not Products are limited by security technology, you agree to use Products in compliance with the applicable Usage Rules.
And, in the Usage Rules:
>The Usage Rules shall govern your rights with respect to the Products, IN ADDITION (emphasis added) to any other terms or rules that may have been established between you and another party.
TL/DR? Apple places ADDITIONAL restrictions on software distributed through the app store. This violates the GPL.
You have this backwards in your post. You say that the GPLv3 prohibits use on the iPhone, but in fact, the Apple ToS prohibits DISTRIBUTION of GPL'd software through the App Store.
End-users are perfectly free to install VLC on their devices. They aren't breaking any laws by doing so. The GPL expressly allows using the software for any purpose. They could install it on a DRM'd toaster if they wanted to. However, DRMOaster Inc. can't distribute GPL'd software.
Instead of modifying its ToS to be more user-friendly, Apple decided to pull VLC from the app store. It could have gone differently.
(quotes pulled from https://www.fsf.org/blogs/licensing/more-about-the-app-store...)