### 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), Rect2i());
	const WindowData &wd = windows[p_window];
	return wd.parent_safe_rect;
}
void DisplayServerWindows::popup_open(WindowID p_window) {
	_THREAD_SAFE_METHOD_
	const WindowData &wd = windows[p_window];
	if (wd.is_popup) {
		
		List<WindowID>::Element *C = nullptr;
		List<WindowID>::Element *E = popup_list.back();
		while (E) {
			if (wd.transient_parent != E->get() || wd.transient_parent == INVALID_WINDOW_ID) {
				C = E;
				E = E->prev();
			} else {
				break;
			}
		}
		if (C) {
			_send_window_event(windows[C->get()], DisplayServerWindows::WINDOW_EVENT_CLOSE_REQUEST);
		}
		time_since_popup = OS::get_singleton()->get_ticks_msec();
		popup_list.push_back(p_window);
	}
}
void DisplayServerWindows::popup_close(WindowID p_window) {