Another one of the projects for 3.2 is improvements to the messaging and notifications UI.
The project page is here: https://docs.moodle.org/dev/Messaging_Notifications_Project
The tracker issue is: MDL-54682
In my test moodle site v3.2 with boost theme, it seems that notifications are automatically marked as read when internal instant messenging is disabled.
Has anyone noticed that too?