Hello!
Sorry for the late reply; thank you for leaving a comment.
If you visit this link, you will see the function _update_click_polygon, which updates the mouse_passthrough_polygon property of the Window with every physics frame via the _physics_process call. Basically, the mouse_passthrough_polygon property decides which part of the screen is rendered and clickable at the same time. I hope this helps!
I rarely check itch.io about this project since it is on GitHub. I can provide further help on GitHub via issues if you happen to need more in the future!