That's one of the things that's reported better in straight G&K than it is in the UP, and could be a factor. But I am pretty sure that terrain happiness is global happiness, because it's primarily for natural wonders in the base game. I'm also pretty sure that no matter what, the reported "your empire is X points happy/unhappy" number should be Completely Accurate, and the fact that there's a different number reported in my culture-per-turn popup is a bug.