How about making them a brutal pick, never allow them to seed by chance anywhere (unless the AI is a fortress baron, which gets a smallish chance to get to chose a superfort on places they would be allowed to get a high mark fort, but even for them it would be HW only), so only by brutal pick or by buy from a zenith trader can they get superforts on their homeworld.
In return, maybe a Mk. IV fortress can be introduced that can get the current AI seeding rules of the superfort (this includes the fortress baron except for homeworld seeding), with the exception that superforts are not allowed to be concurrently picked on the same planet during game seed (not sure about zenith trader buys yet)
Also, replace the superfort astro train construction project with the Mk. IV fort construction project.
Unlike the AI superfort, the AI Mk. IV fortress would have the reduced range like the other AI forts.
The idea would be that the AI superfort becomes a brutal pick or zenith trader exclusive (with only fortress baron being an exception, and even they would be restricted to placing it on homeworlds at game seed), but still giving a "high tier" fortress for a rare seeding for the rest of the galaxy. (Of course, some way to build a Mk. IV human fortress will need to be added
)