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i use buffs indiscriminate of the calculations as stated above. I see it as stopgap measure/push to compensate for lack of licenses. so i basically use em to push yield on resources needed down the line and/or expensive resources (like goldmine). I prefer to use em on 3 times 9 or better) upgraded buildings as this boosts the net yield of the buff the most. I will stop production to stockpil items so when i pop a big buff, i am assured i will have all needed materials to use the buff to max effect.
Oh- and i try to keep my lvl 3 fishers buffed with fish buffs as much as possible as that increases the yield on fish production by around 70% and i dont lose other stuff. Bread is far more valuable to me for making settlers than buffs tbh- so 75% + will go to that, rest is a combo of buffs and fishfood