I tend to have several tabs to a phabricator instance open.
Lets say you have 2 tabs, A, B
You get some notifications. the Title and Notifications icon show (3) notifications
On tab B I click and select mark all as read.
Tab A still shows a (3) in the title and on the notifications icon.
Clicking mark all as read should affect the other tabs as well.
This only applies to realtime notifications.