I'm not sure I follow you.
I mean that your Arduino sketch sends the output that is intended to perform a gear shift, and for whatever reason it doesn't manage to perform the shift, or doesn't shift at all, or there's an electrical glitch and what you thought was one pulse ended being broken into two pulses and you shift two gears. Without any feedback at all, your sketch has no idea whether that pulse actually engaged the next gear; you could be left in the original gear, or neutral, or somewhere else. You can design and test all you want, but Sod's law is inescapable.
That is true. I don't think the system will be able to fail in that respect though. The Pingel shifter is pretty reliable.