### 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
SetCursorPos(pos.x, pos.y);
			SetCapture(wd.hWnd);
			_register_raw_input_devices(window_id);
		}
	} else {
		
		ReleaseCapture();
		ClipCursor(nullptr);
		_register_raw_input_devices(INVALID_WINDOW_ID);
	}
	if (p_mode == MOUSE_MODE_HIDDEN || p_mode == MOUSE_MODE_CAPTURED || p_mode == MOUSE_MODE_CONFINED_HIDDEN) {
		if (hCursor == nullptr) {
			hCursor = SetCursor(nullptr);
		} else {
			SetCursor(nullptr);
		}
	} else {
		CursorShape c = cursor_shape;
		cursor_shape = CURSOR_MAX;
		cursor_set_shape(c);
	}
}
DisplayServer::WindowID DisplayServerWindows::_get_focused_window_or_popup() const {
	const List<WindowID>::Element *E = popup_list.back();
	if (E) {
		return E->get();
	}
	return last_focused_window;
}
void DisplayServerWindows::_register_raw_input_devices(WindowID p_target_window) {