Well, there are certain parts of that game that are phased. Very often, once you're done with a certain quest chain, certain aspects of the zone change for your character to reflect your accomplishment.
Then again, this game isn't in any way better in that regard. The rakghouls on Taris are still there and the cult on DK didn't go anywhere.
Either way, in my opinion, it's better than every agent being Agent Nine and every bounty hunter being the champion of the great hunt.