Thanks for making an effort to teach the AI how to play the game. I had no idea it suffered so much from rushing facilities and SPs. Seems very counter-productive to give the AI all those bonuses on Transcend level, only to take them away in another part of the game. So I'm guessing it might have been a bug?
What I would like to see would be a change in the rules as to where boreholes can be built. Not allowing them on slopes by making it impossible to build boreholes in tiles with lower land next to them should also make it impossible to build boreholes right next to sea tiles, since those by definition are lower than the coastal tiles. Instead coastal tiles are perfect for boreholes, which seems very wrong. Particularly for single tile islands, where it looks like a borehole is in the middle of the ocean. But I understand that I might be alone in this, and/or that it might be too difficult to change. (Though I wonder if the AI is using those rules, and thus has a lot more difficulty finding good spots for boreholes.)
It would also be nice if a borehole would collapse if the tile it is on becomes a slope. But that seems impossible to arrange, as no terraforming is ever destroyed by height/depth/rockiness alterations, as long as the tile doesn't change from sea to land or vice versa.