Clickthrough enabled while still capturing mouse movement?

Godot Version

stable-3.6

Question

Hi there! I really am not sure which category would be best so I'm shooting my shot here. I am trying to make a "taskbar ball pit", where a amount of orbs rests at the bottom of the screen at all times. The orbs have physics and can disturbed by your mouse. The issue I am running into is that I cannot keep the window always on top while still being able to use my computer by having mouse passthrough enabled. Additionally, my mouse movements are no longer registered to move the balls around with due to the passthrough, which makes the entire project nonfunctional. Is there anything I can do to realize this idea?

Set Always On Top in the Project Settings → Display → Window → Always On Top
Or did you? it’s not mentioned lol.

Oh! Yeah I have activated “Always On Top”, but it still goes into the background when I click…

I have never tried this myself, have you tried using Input.get_mouse_position(), or something similar in a physics process function?