Suong being OP is only temporary. So far there are no consequences for joining any of the main characters so I decided to give the player powerful companions. As I expand the main quest, you will have to do more to get the powered up Suong, the generals, or to access Mr. White's shop.
As for the boss, the soviet bunker is randomly generated to a degree. It consists of roughly five locations and each location has three variations. It's quite possible that there is one variation of that room where the boss sprints after you.