In the feature list on the game's web site it say's...
That site is owned and run by Micro$oft.
And you actually BELIEVE anything it says there?
Here is a little tip...
If you ever see "M$" say ANYTHING about ANYTHING assume it is a lie....then you will never be disappointed.
Basically, to answer your question, they bent the truth a bit, or at least state things in a way to make it seem like you actually have options that you truly do not.
In the single-player game you have to attack a base in the first missions, well you actually have to take out it's weapons platforms and another wing of ships destroys it with torpedos...that is an example of "deciding to destroy a pirate base" of which they speak.
The only times you will "destroy a base" is if the stroyline says you do.
You will probably hear the excuse "well they can't let you destroy all the bases because what happens if you have to meet Juni at a base and you destroyed it!". My reply to that is: Other games, like Morrowind, allow you to do things which may make the storyline unfinishable, why does this one treat the players like morons?
If anything, letting you possibly destroy something needed for the story to proceed offeres MORE realism to the game, and offers MORE replayabilty value.
Over-Hyped, Under-Realized.
Anyway, I hope this has answered your questions.
Fly well,
Pyrate Dredd