### 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
POINT coords;
				coords.x = mb->get_position().x;
				coords.y = mb->get_position().y;
				ScreenToClient(hWnd, &coords);
				mb->set_position(Vector2(coords.x, coords.y));
			}
			mb->set_global_position(mb->get_position());
			Input::get_singleton()->parse_input_event(mb);
			if (mb->is_pressed() && mb->get_button_index() >= MouseButton::WHEEL_UP && mb->get_button_index() <= MouseButton::WHEEL_RIGHT) {
				
				Ref<InputEventMouseButton> mbd = mb->duplicate();
				mbd->set_window_id(window_id);
				last_button_state.clear_flag(mouse_button_to_mask(mbd->get_button_index()));
				mbd->set_button_mask(last_button_state);
				mbd->set_pressed(false);
				Input::get_singleton()->parse_input_event(mbd);
			}
		} break;
		case WM_WINDOWPOSCHANGED: {
			Rect2i window_client_rect;
			Rect2i window_rect;
			{
				RECT rect;
				GetClientRect(hWnd, &rect);
				ClientToScreen(hWnd, (POINT *)&rect.left);
				ClientToScreen(hWnd, (POINT *)&rect.right);
				window_client_rect = Rect2i(rect.left, rect.top, rect.right - rect.left, rect.bottom - rect.top);
				window_client_rect.position -= _get_screens_origin();
				RECT wrect;