I really see what Apple is trying to do here - I do not want a system as in Windows, where my Game Launcher X scans my hard drive for other game launchers, and extracts contacts & game list just to send it to Game Launcher X manufacturers servers for "analytics" or "enhancing my user experience". (this is just an unconfirmed rumour but nonetheless, see [0])
Apps have become far more than just programs and tools we use to solve a problem, they have become marketing channels and data-gatherer for the companys creating them. The time we can install a program from a trustworthy source and give it full access to OS APIs and the Filesystem are gone.
I do not have a better technical solution as what Apple shipped, but I really am glad that I can prevent Applications from scanning through my Downloads folder or settings folders of other applications.