Let me see if I can make sense of this...
If you want to build a Windows 8 application, you need to target the WinRT runtime or no runtime at all. Targeting WinRT will of course give you access to the platform features, where targeting no runtime at all will not (basically you would create an application that can run on its own but not do anything really interesting). So, in the interest of keeping this conversation topical, let's consider a Windows 8 application an application that target Windows 8 features, hence WinRT.
Now, you can choose the way you target WinRT. You can use the "managed way", with C#, XAML, C++, or you can use the "web way" with JavaScript, HTML and CSS. All these technologies are first citizens in the Windows 8 app model.
When you build a PhoneGap application, you're not targeting Windows Phone or iOS or Android or Blackberry. You target the PhoneGap runtime. And you can target that by using JavaScript, HTML and CSS, but just because you're using "standard" technologies, it doesn't mean that your PhoneGap app will run, say, in FireFox. It will run in the PhoneGap managed runtime.
Same thing for Windows 8. Even if you use JS/HTML/CSS, it doesn't mean that your app will run in any browser. Unless it's a very trivial app, it will use *something* from the underlying platform and will, by this, be platform dependent.
So, making the "web way" a first citizen in the Windows 8 app model is not the same as saying that a Windows 8 app developed in this manner will be usable (or even meaningful) in an arbitrary browser. Even using prefectly standard JS/HTML/CSS, if an app targets WinRT, it is a Windows 8 app.
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