### 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
_THREAD_SAFE_METHOD_
	ERR_FAIL_COND_V(!windows.has(p_window), Point2i());
	const WindowData &wd = windows[p_window];
	if (wd.minimized) {
		return wd.last_pos;
	}
	RECT r;
	if (GetWindowRect(wd.hWnd, &r)) {
		return Point2i(r.left, r.top) - _get_screens_origin();
	}
	return Point2i();
}
void DisplayServerWindows::_update_real_mouse_position(WindowID p_window) {
	ERR_FAIL_COND(!windows.has(p_window));
	POINT mouse_pos;
	if (GetCursorPos(&mouse_pos) && ScreenToClient(windows[p_window].hWnd, &mouse_pos)) {
		if (mouse_pos.x > 0 && mouse_pos.y > 0 && mouse_pos.x <= windows[p_window].width && mouse_pos.y <= windows[p_window].height) {
			old_x = mouse_pos.x;
			old_y = mouse_pos.y;
			old_invalid = false;
			Input::get_singleton()->set_mouse_position(Point2i(mouse_pos.x, mouse_pos.y));
		}
	}
}
void DisplayServerWindows::window_set_position(const Point2i &p_position, WindowID p_window) {