Windows can't be transparent so xkbd is setting the background to black and then drawing your transparent image. A new window inherits the content below it and might appear transparent before you draw anything. Problem is that it doesn't continuously inherit that content so you only get an initial snapshot. It also picks up any content drawn over the window as well, so the right side of notifications would appear to stay on the screen after the left side disappears.

You'd have to write an app that opens a 1x1 pixel window and intercept all taps. Any taps on the left side would be passed through to windows below it and taps on the right side would invoke an action such as generating a key event and passing it through to the window below it. You can google for some sites that teach C and xlib programming, and make yourself a simple app in no time at all.