The reason that you cannot board a ship that is on autopilot is simply that it is not a player ship. It is an AI ship, and therefore does not have an icon on the left side of the screen. You must board the ship while it is a player ship before it becomes an AI ship.
In SSE there is no real difference between Autopilot and AI: All AI ships are running on autopilot. All “player†ships that are running on autopilot are AI ships.
In the demo, you can leave the Cutter in the RIB, but cannot return.
However, in the ME it is possible to make the Cutter a player ship when the RIB is deployed, thus allowing you to retrieve the RIB. But, you would need to do something to keep the Player Cutter from getting into trouble with no one at the helm. You would need to bring it to a complete stop before switching it from AI. That would only work if Cutter was stopped when she became AI because when an AI ship goes back to being a player ship, she resumes the speed that she had as a player.
Or, you could leave Cutter as AI until the RIB returned within a certain distance. Lots of fun.