Well, WCS (including WCS for FSO) obviously uses it, and I remember seeing it used once or twice in Aftermath Reboot and an older mod called Twist of Fate. So it can be done in regular FS2 somehow.
I think there is some confusion going on here about Battuta and my replies. It's also been many years since I played WCS so I might be misremembering something. Basically there are two ways to achieve an autopilot effect in FS2_Open.
1) Fake an autopilot effect. Basically you have the player choose nav points etc and then when they click activate the game plays an in-game cutscene that was handcrafted in FRED by the mission designer. While that is playing, the player and any ships that are in their group are teleported to near the nav point using SEXPs.
2) Use the built in autopilot tools. When you hit activate the AI will take over the ship and you and any grouped ships will form up and fly in the direction of the nav point. The game will then activate a time dilation effect and speed up until the player is close and then slowly move back down to normal speed.
The WCS requested built in tools which were coded in by Kazan if I remember correctly. However, they later switched over to method 1) and largely ignored the built in tools, presumably because the flyby animations when activating autopilot are more Wing Commander in style.
If you want to make a mission with the actual autopilot stuff that is coded into the game, I can talk you through a lot of that since I've been using it for Diaspora R2. I've been using them as a placeholder since I also intend to move over to handcrafted flyby animations at some point. So I'm not as familiar with how WCS did those, but I do plan to eventually crack open the WCS VPs and reverse engineer how they did them.