Eric - thanks this definitely helps clarify. I'm going to confirm with the PhoneGap team, but it sounds like PhoneGap leverages what you describe as the WebKit API component on iOS, and likely the equivalent for Android, Blackberry, etc. So in the case of the jQuery Mobile GBS chart, the each operating system's WebKit API component is what's represented.
This make sense as to why the support is similar, but not exact. The PhoneGap team based their interpretation of each OS's browser component on WebKit, but as every implementation of WebKit differs, therein lies the variation.
The good news is, if the PhoneGap team keeps up the good work and sticks with WebKit for each mobile OS, it will be the easiest "browser" to ensure jQuery Mobile is compatible with. It already has more "A"s than any other browser.
Personally, I think the talk about Apple intentionally negatively impacting web apps is nonsense. They added enhanced JS performance for their mobile web browser, which make sense to be higher on the priority list than web apps launched from the home screen, as more people use the iPhone to browse the web than any other device. I think any enhancements will eventually make it to all areas of iOS, but should be seen as enhamcements, not bugs. I'm not worried.