PhoneGap provides, if you include its JavaScript file in your PhoneGap-wrapped web app, JavaScript APIs to the camera, stored photos, the address book, and some other stuff.
Some of this stuff is in 'HTML5', like geolocation, but much of it isn't. Apple could have provided custom APIs to the camera and so on and allowed people to access it from their iOS-specific web apps.
The way that an API gets to be a standard is that someone implements it and people use it - if Apple had included a camera access API in Mobile Safari, it probably would have found its way into a spec and been implemented by other browsers.
Your last question seems confused: HTML/CSS rendering and JavaScript processing is part of the device's OS (in the form of its web browser). No browser does everything that's in the standard, and most browsers do things that aren't in the standard. Just adding it to the spec for HTML5 wouldn't be directly meaningful.
