Hi!, I really love the idea and I enjoyed the video a lot. It inspired me to work on something. After doing some searching around trying to solve the click-through screen thing. I found this addon (for godot mono) that does the job.. but only for windows tho, I thought I would share it with you if you ever decided to revisit the project. Maybe you could build on top of the addon to add Mac/ Linux support. This would complete remove the pain of having to use multiple windows (which gets rid of the weird white borders glitch)
Good luck with future projects and I hope you have a good day! :D