If you want to mimic the Gmail behavior of selecting the next older message after archiving (MailMate by default selects the message above the one you archived if you're sorting from newest to oldest), you need to toggle this hidden preference:
defaults write com.freron.MailMate MmMessagesOutlineMoveStrategy -string 'previous'
This is posted in the MailMate bug tracker, but I wanted to post again here to potentially enhance googleability.
Update: this is also posted on the official documentation page for hidden preferences.
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