Denying those prompts when you’re unsure is not a bad default position, usually the app will provide a message explaining why it is asking for access to something. When an app wants to access a restricted resource, such as files outside of its own container, it must get permission from the user and the user can decide if they want the app to be able to access it. The app should handle denial appropriately.
Running the defaults command in Terminal is a bit of an unusual case, to change an app’s preferences requires access to that app’s container and it’s not actually Terminal doing it but rather something else running inside it (defaults) which Terminal knows nothing about, which is why Terminal has to ask for (temporary) full disk access without being particularly informative.