Some feedback:
1. The Autonomous AI Battlestation is invisible without the skill. Ideally it would always be visible, but unbuildable without the skill.
Also, I am unsure if it is intended to be much cheaper in both time and money compared to the vanilla Star Fortress.
Star Fortress = 390 days + 1,750,000 credits
AI Battlestation = 120 days + 500,000 credits
2. The Gene Lab building states the completion as a percentage. It would be useful to have a time as well. Also perhaps add this information, and the "stalled due to artifact shortage" message to the terraforming project menu.
3. With all terraforming projects enabled, the new terraforming system feels like issuing console commands through a menu rather than a mechanic integrated into the game. The choices also vary wildly in power but all require consumption of the entire EUTECK. I have no good ideas to improve this, though. As you said, unrestricted terraforming is very difficult to balance, and I will be playing with it disabled anyway. Despite these problems, it's great that you implemented it for people who prefer it. The Paradise world looks pretty good, too.
Domed Cities is not a straight upgrade - the ground defense malus makes invasions trivially easy once the orbital station is destroyed. This mod is intended to be used in conjunction with Nexerelin, where the player's planets face the threat of invasions.
I would say that Domed Cities are a straight upgrade.
1. It suppresses the hazard effects of various planetary conditions without removing them, so that you can still use the vanilla industry items.
2. It provides a small but useful passive growth bonus. Suppressing negative conditions also reduces the price of hazard pay, indirectly increasing growth.
3. Slotted AI cores add stability. Stability increases fleet size and counters maluses such as Free Port.
Even with Nex, it is unlikely that the AI factions will be able to successfully invade the planet. Usually they die to the station+patrols, and are almost guaranteed to die if the player fights alongside the station. The large ground defense malus was never a factor in my 6.0.0 game, since they always died in orbit.