If you scroll through the replies, he does admit to opting into a feature to integrate SMS and phone with Messenger [1].

No doubt there's a permissions/version and facebook-overstepping-ethics conversation to have here (as always), but this isn't as major as the title implies. It does seem like Facebook continuing using permissions after he opted-out.

[1] https://twitter.com/dylanmckaynz/status/976825435026735104