So to be clear you want such a program to be implemented to be running as root in a way that the user can't individually control its just another root daemon that the user may or may not be aware of.
craftinator wanted a way to log his/her own keyboard events.
Of course a custom extension can also be created for this use-case, in which way the compositor can allow/deny access for keypresses to specific windows. But to be honest a central hot-key manager where apps can register new bindings (and with compositor managed multiple bindings resolution instead of the ad hoc way under X) would be a great target.
That's one way to do it, it's probably not the best way but it would work if you were planning to sidestep Wayland security completely. You could make it user controllable with dbus and then make a GUI to talk to it.
