I've seen the AI use stellar manipulation lots of times. Try playing a "Cluster Wars" game with max AI. Just select a large cluster quadrant map with the option "All Warp Points Connected" deselected. You will get 10-12 isolated clusters of systems. As soon as the AI gets open warp point technology, the map gets quite confusing
Systems all across the map will be linked together, and there will be portions that will be difficult to see because there are so many warp lines.
I've also seen the AI convert asteroid systems, and create/destroy a few storms. I have yet to see any sun nukes, black holes, or nebulae.
Oh, and this isn't with modded races, all are the standard canned ones. You just need to give them a bit of space and the motivation