Some time ago, I used to be able to set up a mouse binding that would work on all windows. For example I set up a binding for SUPER + mouse wheel up ... and SUPER + mouse wheel down ... that changed window transparency. I now have the same setup, but it ONLY works when I'm pointing at the window's title bar. When I'm pointing at window contents, the binding doesn't work.
Ah sorry for the delay :/
I tried the 2 overlapping windows - I used chromium and an E config dialog. No, the transparency of the window underneath doesn't get altered instead.
Also tried making chromium fullscreen - neither window affected in this case either.
I have noticed this bug doesn't seem to affect E dialogs ( ie I can use keybindings on them while pointing in any of the window content ), but this bug does affect terminology.
Lastly, I've tried T4890, and I can't reproduce this.
I've just tested under wayland, where I can NOT reproduce this bug. So it only appears to affect E running under X. I've also tried under X with software and opengl compositing - and can reproduce either way.