"Web apps that are saved to the home screen do not run within Mobile Safari. They’re effectively saved as discrete apps — thin wrappers around the UIWebView control."
Apple clearly believes that there are important security risks associated with their Nitro Javascript Engine.
I have no trouble at all believing that they have been able to mitigate those concerns for Safari Mobile by using a solution that is not appropriate when applied to any arbitary App that may choose to include a UIWebView.