Make the template app static, sign it with whatever special permissions MobileSafari has. (I'm assuming that some special permission is needed, signed by apple.)
Instantiate the app by copying it and placing the files related to the specific instance (manifest, html, cached files) in the standard mutable data directories (Documents, Cache, ...), which wouldn't affect the signature. (The name of the app and icon would have to excluded from the signature.)
If this is how things work now, I wouldn't be surprised if the lack of Nitro was just an oversight on Apple's part (i.e. they forgot to give the template app the right permissions). If home page web apps are granted a special exception to the usual app-signing, I could imagine that they can't give them these permissions without leaking them to everyone.
Instantiate the app by copying it and placing the files related to the specific instance (manifest, html, cached files) in the standard mutable data directories (Documents, Cache, ...), which wouldn't affect the signature. (The name of the app and icon would have to excluded from the signature.)
If this is how things work now, I wouldn't be surprised if the lack of Nitro was just an oversight on Apple's part (i.e. they forgot to give the template app the right permissions). If home page web apps are granted a special exception to the usual app-signing, I could imagine that they can't give them these permissions without leaking them to everyone.