### 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
case WM_MBUTTONDOWN: {
				MOUSEHOOKSTRUCT *ms = (MOUSEHOOKSTRUCT *)lParam;
				Point2i pos = Point2i(ms->pt.x, ms->pt.y) - _get_screens_origin();
				List<WindowID>::Element *C = nullptr;
				List<WindowID>::Element *E = popup_list.back();
				
				while (E) {
					
					Rect2i win_rect = Rect2i(window_get_position(E->get()), window_get_size(E->get()));
					
					Rect2i safe_rect = window_get_popup_safe_rect(E->get());
					if (win_rect.has_point(pos)) {
						break;
					} else if (safe_rect != Rect2i() && safe_rect.has_point(pos)) {
						break;
					} else {
						C = E;
						E = E->prev();
					}
				}
				if (C) {
					_send_window_event(windows[C->get()], DisplayServerWindows::WINDOW_EVENT_CLOSE_REQUEST);
					return 1;
				}
			} break;
		}
	}
	return ::CallNextHookEx(mouse_monitor, code, wParam, lParam);
}
LRESULT DisplayServerWindows::_handle_early_window_message(HWND hWnd, UINT uMsg, WPARAM wParam, LPARAM lParam) {