Of course it bypass protection, what do you think it does.
Its designed to only install from store and I doubt that will work on win8 ether.
So can we agree it isn't apple saying it and can we also agree that actually it is a great thing for the vast majority of users to limit apps, to ensure thy work are secure etc and not only that but android has recognized this. Well they knew all along, they just want to limit as least as possible. But due to negative publicity even they have tightened up on it.
Same goes for hardware. Which is why Microsoft is limiting hardware, to try and insure fragmentation doesn't happen and to ease the programming issues which you get with completely open systems.