So my theory is rather simple. First, why was the SIVA engine locked behind laser grids? Because the splicers knew that we could use it. It became a pulse rifle because that is what we used during the quest it got its perks from studying what guardians used frequently in the past; outlaw from fatebringer and the swarms from ghorn. I'm fairly certain that the nanite bullets consume the enemies to create the nanite swarms. It does bonus damage to fallen because that is what we were fighting a lot of and it wanted to be as useful as possible. The math puzzles locked our choices into the CPU, and when we turn it in, the nanites build the gun then and there. Please leave comments below I would like feedback on this topic.