Option 1: add an X extension that lets you configure which windows get to see which input events. Most clients don't actually need to see any events besides the ones they would see while in focus, so most clients don't notice.

Option 2: replace X with something entirely different -- different rendering, different input, different IPC, different organizing principles, different programming models -- and patch all downstream dependencies to use it.

If you can't see that Option 2 is clearly more work and more disruptive, I don't know what else to say to you.