Sometimes messages at popups don't need of reply. And will be comfortable to mark them as read.
I propose add check at popup to mark message as read and not open app.
@mubat You can "send" an empty reply (or a single space as a reply) and it will just mark the conversation as read.
@john-preston, it's some QUIRK.
I as window-like user will not know this and I want button that do action.
Also button is more friendly functional.
PS
@mubat I tried to make such button inside a notification first, but the notification started to look very heavy and the attention was completely switched from the notification content. Didn't come up with really good notification design yet with both reply and mark as read functions.
How I see it (Paint-master):

its already using icon for read messages
Looks nice.
related: #1625
Hey there!
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Thanks!
No, I don't lost interest. Just dev team not respond
Most helpful comment
How I see it (Paint-master):
its already using icon for read messages