I do not get any notifications for a new Twitch message in the inbox anymore and I do not get the number box next to the messages box on Twitch.
This cannot be fixed, as it was already tried until Twitch complained: https://github.com/night/BetterTTV/commit/93472a0feeaa8b348a584e22f4e159eb27fd29ce#commitcomment-8681632