### 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
window_created = true;
			break;
		}
	}
	
	
	
	if (!window_created) {
		
		return _handle_early_window_message(hWnd, uMsg, wParam, lParam);
	}
	
	switch (uMsg) {
		case WM_NCHITTEST: {
			if (windows[window_id].mpass) {
				return HTTRANSPARENT;
			}
		} break;
		case WM_MOUSEACTIVATE: {
			if (windows[window_id].no_focus) {
				return MA_NOACTIVATEANDEAT; 
			} else if (windows[window_id].is_popup) {
				return MA_NOACTIVATE; 
			}
		} break;
		case WM_SETFOCUS: {
			windows[window_id].window_has_focus = true;
			last_focused_window = window_id;
			
			_set_mouse_mode_impl(mouse_mode);