We turned off the native app popup. Users should no longer see that when using your mobile community.
The homescreen bookmark behavior has also been modified. We have changed this for Cloud but I was able to get it fixed for your 4.5 instance too. Choosing "save bookmark to home screen" will still add the icon to the home screen but will now open the site in Mobile Safari, which will correctly use the full screen on an iPhone 5. However, any users who have already added the site to their home screen prior to the change will still get smaller screen version until they delete it and res-save it to the home screen.
Awesome, thank you!!