I guess the game doesn't set the tank to crackable until you have the official pbs, which are supposed to be the first ones. It doesn't really matter, you'll go by that area again on your way out.
It's because getting the main pb changes the entity set of the room. The first time you go there's the wave troopers and a couple of turrets. When you return there's more pirates and turrets... so techinically when you go w/o the main power bomb, phazon elite doesn't exist and that's why you can't break him out.