Windows 8 is the natural successor to Win7 and XP. It's the next version of the most popular desktop OS in the world. As with Windows 7 and OSX, it should run whatever the hell the machine's owner wants it to. iOS is a locked-down, consistent, homogeneous user experience on specialty devices that should not be and are not marketed as replacements for computers. Apple Store employees will specifically advise against p…
That doesn't mean you should lockdown all the browser apps just to ensure your control. Both iOS and WP8 allow all sorts of apps to be run. Then why not another browser? AAPL's insistence for banning flash was justified. Flash has always been memory hog and battery killer but not allowing non-webkit browsers is foolish.
What is not allowed is to download code and execute it, which makes it impossible to write your own JavaScript interpreter, and forces you to use UIWebView to render HTML. You can't even just use webkit on your own -- you have to use the one on the device (by using UIWebView).
FireFox would also not be able to have plugins for similar reasons.
Atomic is better than Safari because it allows User-agent switching, view source and some other nice features, all of which doesn't require them to interpret JavaScript with their own code.