I initially thought you were just splitting hairs, but seeing as you've used this argument somewhere else in this thread I think this might be a genuine thought you have so I will take the time to explain why home-screen web apps are absolutely nothing like other native apps on the system, and actually essentially the same as loading a web page in MobileSafari. So for starters, let us observe that there are three instances where JS can run on iOS that we care about:

1. MobileSafari, from a web page loaded from a URL.

2. Home-Screen Web Apps, web pages loaded from a URL that the user then 'saves to the homes screen' which are loaded in some mysterious, but APPLE WRITTEN, "wrapper" process X.

3. UIWebViews within native apps that you buy on the App Store.

Now, my position is that (1) and (2) are for all intents and purposes the same, and (3) is possibly different. So, the whole argument about turning it off for UIWebView is that the interaction between native code and Nitro might offer an additional vector of security concern. Well, in both (1) and (2), there is no user native code. It literally just either downloads the JS off the web, or reloads it straight from the web. All the native code is written PURELY by Apple. So in a world where the only user modifiable code comes from the web, then clearly this is the same as where we started with MobileSafari. The additional thing to realize, is that unlike native apps (3), home-screen web apps (2) are NOT code signed, just like web pages (1). So that also nullifies the argument that allowing Nitro on home-screen web apps would go against Apple's code signing policies.

Hopefully that explains my thinking a little bit clearer.

Once again, I am very willing to believe that they had a deadline to meet, and turning it on for home-screen web apps got punted. That makes perfect sense. The security argument however falls flat on its face.