Well, the point of E2E encryption is that you cant bypass it. That only the recipient is able to read it. Believe me that if I start making e2e encryption, no one will bypass it and I doubt the engineers at Apple are not able to do it, unless instructed otherwise.
I will tell you another case: Skype. It had a p2p protocol, highly encrypted and obfuscated, also the application was armored. The communication wasn't going through Skype servers but directly between devices. Once Microsoft bought it, the next version was using Microsoft servers and p2p was gone. Interesting, right?