I highly doubt Messenger will have end-to-end encryption, especially that they have to display those messages on Facebook web.
Also an option to enable web E2E with a password-protected key stored on FB's servers is still pretty darn good.
People are using both Messenger & Facebook web to send messages, they will have to break that somewhere for end-to-end.
If Facebook is storing your encrypted message database on their servers then the problem gets significantly easier.