So I was doing some testing and using observer mode. I noticed a few of the AI empires really struggling so clicked on there capital planet. Then I saw that they were showing way less than 100% habitability on their capital which seem strange and I noticed it seemed to be because the pops had "Gaia World Preference". I'm guessing that for some reason that is overriding the default 100% habitability for capitals. Here is a screenshot showing that the AI empire is pretty much crippled: