At the moment, reading a post does not clear notifications for that post.
What happens very often to me on this forum is that I see new discussions appear on the homepage in real time, I click on it and read it, but don't notice there is a notification.
Then later when I come back to the forum I see there are new notifications, but it's for the posts I already read when they appeared in real time on the homepage.
Unfortunately at the moment we have no way of automatically marking notifications as read based on forum events. The notifications are only marked as read when clicked.