So fatal flaws in various systems and beings will be impossible after certain point? I find it improbable, that every action and move will be perfectly calculated, so it can be executed without any bad consequences. Also we could notice such destruction here or there. In caveman2cosmos military and war still are a thing in Galactic and later era (well there are some military units/buildings/techs). Read description of future civics especially military branch. There are clearly evil buildings like time abyss or roko basilisk too. So in Pepper's vision of future we are most advanced aliens. Also we can spread destruction, if we wanted to till end of game. In your vision of future you can't do misdeeds, and perfect security prevents accidents too. Or at least no one can leave home system without 50 years long training.