The improved email notifications for comments are great, but there's still an issue with them in Gmail.
All emails come from the sender notifications@github.com. The display name of the sender is set to the full name of the commenter, which is wonderful. However, when viewing a list of conversations, Gmail considers all the messages in the conversation to have come from the same sender, and therefore only shows one name in the list of participants. That name is the first display name given, which is the name of the first commenter. The later names are ignored in this view. At the same time, next to the subject line, Gmail shows a message preview of the last message in the conversation (or the first unread message). When this message was not sent by the same person as sent the first message, the list view misattributes the message, and makes it look as if someone has replied when in fact someone else has.
This sounds petty, but it can be quite annoying, for instance, when you believe that the maintainer has replied to your comments when in fact it was only a random passerby saying ":+1:".
Now, the only way to make that not happen may be to use a different sender for each GitHub user. That's problematic because then you'd have to approve showing images for each sender, which I'm guessing is why this happened. If there's any way to make both work, though, I'd really appreciate it, and I imagine I'm not alone.
Better late than never: no you are not alone! This has been annoying me greatly for a long time. Will re-submit this to Github support and hope they will look into it.