I've searched Microsoft's KB, search google, searched Apple, but can't find anything. If I leave the Smart Folder and click on All Accounts > Inbox, I see just the single email. It does not appear to happen with my iCloud account. This seems to happen only to emails received in my Gmail accounts. Whenever I create a new search (or use one of the pre-defined Smart Folder searches), the results come back with each message being listed three times with the same time-stamp, and once without any time-stamp (!). In doing so, I wanted to create an 'Unread' and also a 'Today' Smart Folder so that I could more easily manage my multiple inboxes. I'm switching from Apple Mail to Outlook for Mac 2016.
Application: Outlook for Mac 2016 (Insider Slow and Insider Fast)