During a normal war a system you take is considered occupied but not captured/conquered. You can use starbases to heal once they start repairing themselves but you cant make changes to the starbases and you cant use the shipyards. I think there is also limits to what you can do with the planets. During a total war a system you fully take is considered yours immediately and you immediately have full control over it, the planets, the starbase and can use the shipyards. This is to stop you from capturing a starbase during a quick surprise war, downgrade/destroy it and immediately calling for peace, or avoiding having to fight it again when the system is recaptured, or starting to build/upgrade ships and losing the system because of peace without having to spend influence to claim it. That is why total war is so powerful but requires more hoops for you to jump through to be able to use it.
