I tried to use the new hint using this example. The application works as expected and allows mouse passthrough when running natively on each platform X11 and wayland, i.e., using X11 window on X11 and wayland window on wayland.
When running the same application through Xwayland on KDE plasma 6 wayland, the focus passthrough stops. I can’t seem to find the reason as to why this might be happening, as another person reported that it works fine on their plasma setup and even on Hyprland through xwayland Focus not passed through on click (Wayland) · Issue #11 · coderedart/egui_overlay · GitHub.
Hi @mystchonky welcome to the GLFW forum,
Given that this works with both X11 and Wayland I think it’s possible that the issue with XWayland on KDE plasma 6 wayland is more due to that setup, and I’m not sure there’s anything we can do in the GLFW code to get around this.
Do you know if there are any other apps working on this setup which have working mouse passthrough?
I am not sure about other apps. I will look for some. At the same time, I will go talk to KDE folk about the same 
It was an XWayland issue itself related to https://gitlab.freedesktop.org/xorg/xserver/-/merge_requests/1510.
Fix has been merged in 24.1 and should be out soon
That’s good to know - thanks for reporting and investigating this!