Fallen Spire, Nomad, and Showdown only win the game when the AI Home Command Stations are destroyed; these are just alternate methods to get that done.
That said, you can still move around and do stuff after the "YOU WIN" banner pops up, so you might be able to trigger the special effects of more of these. For example, the Exogalactic Wormholes on the AI's homeworld remain even after the AI is defeated, so you could still use the Blade there.