You're correct that there are different types of encryption that can be done end to end if there's a communication. It can be user-encrypted. It's not just about communication. A user could have their own encryption where the provider does not have the key to that information. There are encryption models where the supplier or provider may have the key to that encrypted data.
I can't speak to the Apple example. I'm not a technical expert in terms of what each company does and how they do encryption.