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.
I don't know... Lucius Fox has demonstrated before that he likes to design things with ejection systems that are vehicles in and of themselves. Catwoman was zipping around on part of the original Tumbler a full 8 years after it was destroyed.
We saw Batman in the cockpit. We did not see the cockpit in the Bat. (Or did we? I was not watching for details like that last night).