I realized that Natural Wonder that came from Gods & Kings and Brave New World DLC isn't properly supported by IGE terrain placement. Not a big deal, but still a minor issue for me.
I also separate Spaceship units and put it inside their own group, and hides it when you turned off Science Victory.
If you don't like Spaceship units being hidden, you can set hideSpaceShipsNoScienceVictory value to false on IGE_UnitPanel.lua file. I put it right at the top of the code, so it's easy to find.
For the rest of previous changes, you can read it here.