Apple's App store has never used .app as an extention.
I'm not sure what you mean when you say Apple's App store has never used .app as an extension. Mac and iOS applications have the extension .app in the the same way that Windows has .exe as an extension. Applications sold in the App Store will have a .app extension to identify them as applications. This extension was adopted when Apple dropped the idea of identifying file types by the information held in the resource fork of files (I guess around the time they introduced Mac OS X in 2001).