Why are food bonuses percentage based? I can understand the +100% food from the Farming Guild, but all the other food production increasing structures are likely to give you fractional amounts of food unless you happen to have enough food resources in the area to produce an even amount of food at that city. As far as I know, fractional amounts of food are completely useless and might as well not exist (although I have seen the computer build housing off of 0.5 or so food and then go into the starvation mode with only ~30 people in a city which had five houses (city population never increased and the computer apparently never found another farm, since the city population never changed until I took it) - though this might have been in 1.09e, and I have not seen it recently, and it was kind of amusing).
Would it be better to have the granaries/irrigation systems/fungal storehouses offer bonuses along the lines of +1 food per food resource connected to the city? All the food resources that I have seen have been +3/5/6 food, so this would not significantly alter the magnitude of the food bonus (with both available food increasing structures built in the city you gain 0.5 food on the 3 food sites, lose 0.5 food on the 5 food sites, and lose 1 food on the 6 food sites, as compared to having both food increasing structures for +50% food - which could be solved by having each food increasing structure give +1 food to each food resource and for having both food increasing structures built include an additional +1 food bonus per food resource).