That seems like saying why use an encrypting password manager at all if you're using full disk encryption, isn't it okay to just keep your passwords in plaintext on your encrypted disk?

Not if you use cloud backup or get a virus.

This isn't how real security works.

There is a concept for 'defense in depth', saying that every component should be secure on its own and not rely on other components.

Encryption only protects files at rest. The vast majority of attacks are against live systems connected to a network, where full disk encryption won't help you one bit. It is a nice extra layer of protection for when a device is lost/stolen, but I don't consider it a primary form of protection for any important data.