From what I can gather from looking into various client application frameworks that use HTML + JavaScript, they essentially do use an implicit "web control" wrapper, as you call it, in the application stack. Calls to native APIs are abstracted in a way to look to the HTML rendering engine like calls to browser plug-ins . Browser plug-ins need not only look like Flash player, right? Just make the entire API look like a plug-in to the HTML rendering engine and you can expose your entire OS to Javascript.

From what I remember from playing with the SDK in Windows 8 CP, you cannot create libraries (i.e. the analog of CREATING a "plug-in") using Javascript. Javascript is strictly limited to front end development. IOW, it's just like with regular web applications. You cannot create plug-ins using Javascript. You can only call plug-ins from Javascript.

Not being able to create reusable class libraries is really the biggest limitation of Javascript programming in Windows 8.