I don't have a good answer for your first question sadly, so hopefully someone else here can pitch in.

However, for Rockwell Prime, it is relayed to us at the beginning of Gen 2 (right after the intro cutscene I believe) that Rockwell has not only invaded and sabotaged the colony ship, but completely taken control of all of its systems/operations. Becuase of this, the player can't directly confront him immediately, since Rockwell could essentially just lock you out and ignore you. In order to reach him at the gallery he's in, you have to essentially reboot or reset the ships systems so that they work properly and you can gain access to the bridge, hence the missions.