I remember that VLC could not get into iOS App Store for the same reason, and the story about it was spun by everyone and their dog. Ffmpeg is there because it doesn’t have this kind of PR, and that’s it.
Different issue. The App Store controversy was because VLC was, back in 2011, licensed under the GPL. One of the VLC developers complained to Apple that the GPL license was incompatible with the App Store distribution model, so it was pulled.
The engine parts of VLC were subsequently relicensed under LGPL-2.1, and the rest of the app under MPL.