There are tons of VLC authors, only one needs to complain. This sounds like it's going to happen sooner or later.
Thus authors of GPL software might have a basis to object to other people distributing their software through the App Store, even if full source is provided. ...at least, this was the rationale given by the FSF when they objected to GNU Go in the App Store:
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