you can also trade troops for ration to reduce their number, if you run out of food, your troops die, and mood tanks a lot from that. so trading troops for ration fixes those issue by alot.
You need both for a full cycle, they both do different things. transporters automate what's already in the nest, and f.shrine automates between your nest and your prison.
Just make sure to not dump all your troops into the formation then. If you have floors that didn't lock those troop types out, then leave some in the reserved. you can also use the save/load formation so you wont have to reset the entire formation every time.