The feature team is still reviewing, there is lots of discussion about this item and I hope to have a decision soon.
55 votesRichard commented
My suggestion is similar, but to replace the current 'X' which dismisses the notification dialog, to have two interactive text buttons. One which reads "Mark as Read" and the other would read "Dismiss".
Mark as Read would both dismiss the notification and mark that conversation as read in the Teams client. Dismiss would just dismiss the notification as the X currently does. Leaving the notification in Teams that their is an unread chat.