A civilization that can unwrap protons and build machines that violate energy conservation inside of them wouldn't need to care about taking over other species as basically all the material and energy of any solar system, regardless of whether it had life in it or not,

it is not obvious that such tech automatically gives large scale terraforming capabilities. Also, I think one of the book premises is that trisolars are stagnant civilization, they achieved some advancements in some areas, but couldn't make breakthroughs in any others. They restarted evolving fast after learning from human civilization.

Furthermore, even in a hostile universe there is much to be gained from alliances, especially for intelligent lifeforms for whom the idea of a "civilization" is not tightly coupled to a specific biological underpinning.

Price of the risk is too high if contact with totally different species won't go well.