James -- The results you see in the Debug tab or in a built app will be unchanged, since they depend on the target device. The Simulate tab does have some issues with the window.screen object, it is not setting those values properly, instead, it is showing what your laptop screen values are, which is the proper behavior of the browser implementation for those values (which is what the Simulate tab is, it's a browser pretending to be a device).
You can use the window.innerWidth and window.innerHeight when in the Simulate tab (you can detect the Simulate tab by detecting the presence of window._cordovaSimulate to make the code conditional). See this example screenshot taken from the "hello cordova" sample and the data shown for the device I'm "simulating" in the associated control panel, from the Simulate tab:
I had upgraded to 3491. I couldn't even see the device information in the simulator tab as you show it. I had also found that I couldn't build ANYTHING. I had ended up completely uninstalling Intel XDK using a professional grade uninstaller and then reinstalling it from scratch. The development environment now works a LOT and I mean a LOT better. The uninstall doesn't do anything to the project folders.