Gaze tracking (GT) is a new technology and will likely change and expand in the future. At this time the GT capabilities are available in UWP only. Because of this they function within the context of your app's window.
To capture gaze for the full screen you can expand your app to full screen. However, it sounds like your intent is to get gaze tracking for the entire system independent of the active window. Unfortunately this is not possible with the current GT implementation.
Do you have a specific scenario where you need access to gaze tracking for the entire system? If so please post it here in the comments. I can pass it along to the GT team so they can be aware of how our devs would like to use GT.