That article seems to be talking about the App Store for iOS (the one you access via iTunes). We're talking about the Mac App Store that provides OSX applications.
Now although the situation might be the same, I'm not definitely sure that it is - for one thing OSX still lets you run unsigned binaries (and thus modification to source code).
Re:Wine 1.6 Released With 10,000 Changes
by icebraining on Friday July 19, 2013 @06:46AM
(#6069326)
Sorry, I got the stories mixed up. In any case, it seems it suffers from the same problem - or at least it did in 2011:
https://adium.im/pipermail/devel_adium.im/2011-January/00797...
http://www.fsf.org/blogs/licensing/more-about-the-app-store-...