My theory?
Since they also have to bring Georgiou back to Discovery's original timeframe in time for her Section 31 show, somehow Georgiou is thrown back into the past on the ship, leaving the crew stranded without a ship in the future. She contacts Tyler (or maybe the Enterprise) to find a solution without alerting Starfleet in general or any remnants of Control in particular that the ship is back, and to find a way to get back to the future to help the crew. But there is none, at least not as directly as with the suit.
So they finally come up with the plan to park the ship in a nebula close to the last position Georgiou knew the crew to be, outfit it with an AI that will maintain the ship and its position, and if necessary actively avoid detection, as a type of time capsule for the crew to find. Or maybe Zora has orders to start flying towards the crew's position once the "time has come". But in these almost 1000 years Zora becomes sentient and independent enough to be able to fudge orders to pull Craft on board because she's lonely.
So, Georgiou is back in the past, Zora exists in the 32nd century, and if she reunites with the crew and they meet Craft later he can express how happy he is for her to have found her crew after all this time.