WhatsApp pulls a similar trick on Android. It's E2E encrypted, but by default backups (done to Google Drive) are not. I think most users never enable encrypted backups.
I wouldn't be surprised if there is a deal with law enforcement, where Apple and Meta can do and advertise E2E chats, but the defaults (which most users do not change) are such that law enforcement can still access them. But yeah, Apple and Google were part of PRISM too, so no big surprise I guess?
If you truly care about privacy, either completely disable iCloud backups or get a GrapheneOS phone. Also use Signal, because they exclude themselves from phone backups by default. So either chats are not backed up or they are backed up through Signal's own E2E backup service.