I'd have to watch it again. We'd have to know the very last moment Nolan cut to a shot of Wayne in the cockpitIf Bruce fixed the autopilot who's to say he didn't eject before the Bat crossed out over the bay? When the Bat is seen flying over the bridge Bruce might already have bailed among the canyon of buildings.
We see that closeup shot of him staring at the sun right before the bomb goes off, and he's clearly still in The Bat.
Okay, so he didn't abandon the Bat while in Gotham. He had to jump into the water