### 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 WINDOW_FLAG_TRANSPARENT: {
			return wd.layered_window;
		} break;
		case WINDOW_FLAG_NO_FOCUS: {
			return wd.no_focus;
		} break;
		case WINDOW_FLAG_MOUSE_PASSTHROUGH: {
			return wd.mpass;
		} break;
		case WINDOW_FLAG_POPUP: {
			return wd.is_popup;
		} break;
		default:
			break;
	}
	return false;
}
void DisplayServerWindows::window_request_attention(WindowID p_window) {
	_THREAD_SAFE_METHOD_
	ERR_FAIL_COND(!windows.has(p_window));
	const WindowData &wd = windows[p_window];
	FLASHWINFO info;
	info.cbSize = sizeof(FLASHWINFO);
	info.hwnd = wd.hWnd;
	info.dwFlags = FLASHW_TRAY;
	info.dwTimeout = 0;
	info.uCount = 2;
	FlashWindowEx(&info);
}
void DisplayServerWindows::window_move_to_foreground(WindowID p_window) {