Keith, given that you are more worried about checkpoints being very much required in Fallen Spire and high level game play, why don't we add a special Fallen Spire turret that is granted on a per planet basis. In fact, make a deploy-able ship that needs to be deployed next to a Fallen Spire City, or given how map layouts can go, within 2 hops of a Fallen Spire city.
Call it a special spire military base or something. Maybe even have it work like a Hive Golem with some sort of Spire craft. So when the Exo-waves hit that planet, they will auto-deploy to strike back, but against normal waves they only act if some sort of condition is hit. Such as the Command station gets blown up or a massive ships enter the system. The Spire expect you to deal with the normal threat, but they will not just stand there forever it if looks like you are knocked out of the system.
Then, rather then making the Factories and Fabs basically immortal, you make it grant them Immunity to damage well it exists. Like a Spire version of the Core sheild network that only works on Fabs, Factories and things like that.
Should the AI hit it hard enough, it can still clear the system. But it makes it a lot less likely that a large wave will just instakill those Factories.