The answer to all your questions is the same as the top answers. It uses ethalon. For cultiral buildings - we know the amount of happines per polished tile of that era cultural building. So it's very easy to know the exact amout of tiles we gain or lose because of this particular production building.That does not tell much to me.
How you convert missing/extra happiness to goods/tile ratio? I mean for LNG you need culture building/decoration that gives 350 happiness and for Algae the other way round? Should it be 1.5 and -3 respectively or do you use current age happiness buildings?
Why in AFE and OFE you have modificators when building do not have happiness effect? (figured out)
What does "Unrefined population" mean and why its the same for all buildings? (figured out)
p.s. Still this ratios does not take into account GB and special buildings and their advantages. And lets be honest 95% of players have those in their cities. I mean this calculator, in spite of its complexity, still does not represent the real situation on servers and thus can't be used reliably.
As for the GBs. You are right. Every city is unique. But the base remain the same for every city no matter how it's done there. Because the base is grounded on the unchanged production buildings.
"unrefined" means how much you need to power the unrefined chain to get the goods to your current era productions building.