As much as I would like to agree with you here, Chocorate is not the one who added poop lakes, sewage, and fertilizer. He also did not make the liquid poop drinkable. You really have to point to powercrystals as the enabler here.
Poop and Sewage are part of any real farm. You can't blame a guy for bringing a little realism.
Poop to fertilizer makes more sense to be then mining for it.