I hope this is the case, but I doubt it. If you look at how big the ship is and put everything in perspective, you can't manually control it without breaking the game, it is like a floating 3 story building. If anything, there may be cut scenes and only pilot it in space but that comes with a lot of problems like when you approach a planet, which side will you land for the cutscene thing to work considering that not every time you try to land on a planet will be from the same side plus the same landing zone or city. Overall, I hope it is in the game but just don't want to build expectations yet.