Basically, they need to allow developers to deploy desktop applications through the Store, but provide a way for the application to be installed using AppX to get the benefit of a minimal impact installation. If I were to see a desktop app on a website as well as in the store, then I'd be much more likely to install it from the Store because it's less of a pain. The store manages the install, the updates, and the uninstall. I don't have to remember to check back for a new version, or put up with the application whining about an update. I'm looking at you Acrobat Reader. I think I'm 6 months behind in the reboots that it wants to do. I also know that the developer was required to publish a manifest of what the app needs.