### Godot version

4.0.beta12

### System information

Windows 11, RTX 3080

### Issue description

When a Window Node is created with it's Transparent flag set to true and Project Settings --> Display --> Window --> Subwindows --> Embed Subwindows is false, the Window has a black background. By cycling the transparent flag from false and back to true again, during runtime, the window's background then becomes transparent. 

### Steps to reproduce

Attempt to create a Non-embedded Subwindow with a transparent background using the appropriate flags. 

### Minimal reproduction project

Note: this project is from Reddit user [gongpha](https://www.reddit.com/user/gongpha/) and his Reddit post [Learning a Godot 4.0 Window node](https://www.reddit.com/r/godot/comments/xr8yxn/learning_a_godot_40_window_node/)

https://github.com/gongpha/godot4-window-test
break;
			}
			DisplayServer::WindowID receiving_window_id = _get_focused_window_or_popup();
			if (receiving_window_id == INVALID_WINDOW_ID) {
				receiving_window_id = window_id;
			}
			Ref<InputEventMouseMotion> mm;
			mm.instantiate();
			mm->set_window_id(receiving_window_id);
			mm->set_ctrl_pressed((wParam & MK_CONTROL) != 0);
			mm->set_shift_pressed((wParam & MK_SHIFT) != 0);
			mm->set_alt_pressed(alt_mem);
			if ((tablet_get_current_driver() == "wintab") && wintab_available && windows[window_id].wtctx) {
				
				if (windows[window_id].last_pressure_update < 10) {
					windows[window_id].last_pressure_update++;
				} else {
					windows[window_id].last_tilt = Vector2();
					windows[window_id].last_pressure = (wParam & MK_LBUTTON) ? 1.0f : 0.0f;
					windows[window_id].last_pen_inverted = false;
				}
			} else {
				windows[window_id].last_tilt = Vector2();
				windows[window_id].last_pressure = (wParam & MK_LBUTTON) ? 1.0f : 0.0f;
				windows[window_id].last_pen_inverted = false;
			}
			mm->set_pressure(windows[window_id].last_pressure);
			mm->set_tilt(windows[window_id].last_tilt);
			mm->set_pen_inverted(windows[window_id].last_pen_inverted);
			mm->set_button_mask(last_button_state);