The Bio-enhancer loaded her cells with energy. It's "stored" in them, so she can grow at will even without the device. That explains why she really doesn't choke at 3 miles (and even at greater size). Her cells are fed with energy, replacing the need for oxygen.

The missles would have killed her, but their payload wasn't big enough. Luckily she was able to grow in time, otherwise they would have.

lol OK, I'm making this all up now. Damn, you're stern ;). I'll take care my next story will "explain" everything.