I even went so far as to completely uninstall Start11 v2 with Revo Uninstaller to make sure that every single piece of Start11 was removed and reinstalled the beta version to see if it fixes it. Nope, it doesn't.
So right now, autohide works as intended as long as there's a window on the screen. It can be any window be it the Start11 config screen, a Windows Explorer window, Microsoft Edge, or Calculator. Yes, any window will do. As long as a window is open on the screen and not minimized, autohide works as intended. However, a blank desktop with just the desktop and nothing open on it showing nothing more than your desktop icons will cause autohide to not function properly.