Much work is being done on Wayland compositors and window managers to change this. Among other expected results are also the security aspects where the user is able to know which program is reading certain inputs and outputs, and might be able to control this data. As a basic example, a desktop app is only able to read/write the pixels inside the rectangle assigned by compositor, and it only receives keyboard events and mouse clicks that were sent inside this rectangle. I think this is an assumption one could make about a modern desktop. Sadly not enough users care about this type of security, so we stick to the old, X11 style of altruistic desktop computing where every program can see everything.