It appears they derive the chunk encryption key from the chunk content, so dedupe will be possible if they don't randomize the IV or nonce ([0], page 53). The guide also mention convergent encryption, which would confirm this. Personally, I find it sketchy privacy wise.
These types of busy-work machinations are often done by cloud providers around encryption. The purpose is apparently to say they use ciphers but also keep the keys in order for decrypting data.
Cloudkit and iCloudDrive use Account Keys, but it isn't clear if those are key encryption keys or data encryption keys. It also isn't clear if those are protected from information only from the client, or if the cloud is able to freely read them. The differences are massive in regards to privacy, and this document really doesn't have the needed technical information to make an informed decision.
[0] https://www.apple.com/business/docs/iOS_Security_Guide.pdf