I use Mozilla Firefox, and have had no problems with the ‘mark all read’ feature. I select the messages tab and hit mark all read, the notifications number reduces right away, then I move to the activity tab and do the same, and its all clear instantly each time.
This ‘upgrade’ is, in all probability, a planned move by the site, and it isn’t going away. The least they could do for us creators is move the Activity tab as the default, and the other two useless (for creators) tabs as second and third.