Which encryption model (single-key, per-file-key) does APFS use after 10.13 upgrade
Hey you asked this a while ago but I asked the same question on the Apple community discussion board recently and apparently we were just misreading that documentation. 

APFS uses both single-key and multi-key encryption models simultaneously. The single-key system encrypts the container, and each file within it is encrypted with its own key pair.