### 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 (!wd.event_callback.is_null()) {
		Variant event = int(p_event);
		Variant *eventp = &event;
		Variant ret;
		Callable::CallError ce;
		wd.event_callback.callp((const Variant **)&eventp, 1, ret, ce);
	}
}
void DisplayServerWindows::_dispatch_input_events(const Ref<InputEvent> &p_event) {
	static_cast<DisplayServerWindows *>(get_singleton())->_dispatch_input_event(p_event);
}
void DisplayServerWindows::_dispatch_input_event(const Ref<InputEvent> &p_event) {
	_THREAD_SAFE_METHOD_
	if (in_dispatch_input_event) {
		return;
	}
	in_dispatch_input_event = true;
	Variant ev = p_event;
	Variant *evp = &ev;
	Variant ret;
	Callable::CallError ce;
	{
		List<WindowID>::Element *E = popup_list.back();
		if (E && Object::cast_to<InputEventKey>(*p_event)) {
			
			if (windows.has(E->get())) {