They have that handled by end game disasters... each choice you make, be it research or decisions in planets you discover, has a risk of triggering the disaster... it has been teased that it could be robotic uprising, opening a hole to another dimension, waking up an ancient insectoid master race...
it does, however they did tease about large ancient and advanced empire that lie dormant since they evolved passed meddling into inferior races, they hold special tech that you will have trouble defeating and will be a fearsome for if triggered, but if you reverse engineer they tech, you get some special boons![]()
About ancient empires, there was a line on the wiki that current expanding space faring empires can also become fallen empires. Not sure how that mechanic would work vis a vis universe generation.