You can upgrade your city where there is the rice exchange , this particular province will become "-3 food " for example , but if you have 4 other +1 food regions , your "global food supply" will be +1 , so you'll have no revolts in your "-3 food" region with rice exchange and castle upgrade
The thing is you cannot have all your regions upgraded , you need to keep some regions retarded with just the basic fort , so that they give you plenty of food , so you can build citadels and rice exchanges elsewhere .
But honestly , don't bother with rice exchange , only clans with no trading ports can benefit from it , with Tokugawa you have ports , just spam 40 trade ships to 4 trade nodes and you'll be filthy rich , better keep your peasants happy as long as each family give you their healthiest son to die for your daymio's armies