### 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
DisplayServerWindows *ds_win = static_cast<DisplayServerWindows *>(DisplayServer::get_singleton());
	if (ds_win) {
		return ds_win->MouseProc(code, wParam, lParam);
	} else {
		return ::CallNextHookEx(nullptr, code, wParam, lParam);
	}
}
DisplayServer::WindowID DisplayServerWindows::window_get_active_popup() const {
	const List<WindowID>::Element *E = popup_list.back();
	if (E) {
		return E->get();
	} else {
		return INVALID_WINDOW_ID;
	}
}
void DisplayServerWindows::window_set_popup_safe_rect(WindowID p_window, const Rect2i &p_rect) {
	_THREAD_SAFE_METHOD_
	ERR_FAIL_COND(!windows.has(p_window));
	WindowData &wd = windows[p_window];
	wd.parent_safe_rect = p_rect;
}
Rect2i DisplayServerWindows::window_get_popup_safe_rect(WindowID p_window) const {