### 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
if (!old_invalid && coords.x == old_x && coords.y == old_y && windows[window_id].last_pressure == pressure && windows[window_id].last_tilt == tilt && windows[window_id].last_pen_inverted == inverted) {
						break;
					}
					windows[window_id].last_pressure = pressure;
					windows[window_id].last_tilt = tilt;
					windows[window_id].last_pen_inverted = inverted;
					
					if (!windows[window_id].window_has_focus && mouse_mode == MOUSE_MODE_CAPTURED) {
						break;
					}
					Ref<InputEventMouseMotion> mm;
					mm.instantiate();
					mm->set_window_id(window_id);
					mm->set_ctrl_pressed(GetKeyState(VK_CONTROL) < 0);
					mm->set_shift_pressed(GetKeyState(VK_SHIFT) < 0);
					mm->set_alt_pressed(alt_mem);
					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);
					mm->set_position(Vector2(coords.x, coords.y));
					mm->set_global_position(Vector2(coords.x, coords.y));
					if (mouse_mode == MOUSE_MODE_CAPTURED) {
						Point2i c(windows[window_id].width / 2, windows[window_id].height / 2);
						old_x = c.x;
						old_y = c.y;
						if (mm->get_position() == c) {
							center = c;
							return 0;