E-Mails have 2-staged flag options for levels of 'seen':
Unseen/Seen and Unread/Read.
A message is unseen if it has arrived since the last time we had mutt
open. We do not have to have had the actual message open for it to be
marked seen (or 'old'). In other words, whichever messages we have seen
once on the index alone are not 'new' to us anymore, they have been
seen.
On the other hand, a message is only read if it is actually opened. So
even if we have seen it on the index page, or moved it to a different
mailbox or anything else, it can still be unread if we did not open it.
Additionally, I have it set up now so that the message only gets set to
'read' by neomutt after it has been open for 1 second.
This gives a tiny grace period if we are scrubbing through mails or
accidentally opened one we did not want.