On the physical device, iPhone 6 Plus's main screen's bounds is 2208x1242 and nativeBounds is 1920x1080. There is hardware scaling involved to resize to the physical display.
On the simulator, the iPhone 6 Plus's main screen's bounds and nativeBounds are both 2208x1242.
In other words... Videos, OpenGL, and other things based on CALayers that deal with pixels will deal with the real 1920x1080 frame buffer on device (or 2208x1242 on sim). Things dealing with points in UIKit will be deal with the 2208x1242 (x3) bounds and get scaled as appropriate on device.
The simulator does not have access to the same hardware that is doing the scaling on device and there's not really much of a benefit to simulating it in software as they'd produce different results than the hardware. Thus it makes sense to set the nativeBounds of a simulated device's main screen to the bounds of the physical device's main screen.
iOS 8 added API to UIScreen (nativeScale and nativeBounds) to let a developer determine the resolution of the CADisplay corresponding to the UIScreen.