There's a save comment button for that purpose (to reply later). Saved comments are sorted by time of saving.
You can even create draft comment replies and save them for later.
Clicking mark as unread in the same spot as where the mark as read button appears would be more intuitive
The post/comment reply box isn't an email one, it's a notification box. If you want to reply to a specific comment at a specific time, you can use the save comment option.
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