Outlook for Mac 2016, Gmail accounts and Smart Folder / Search showing message more than once
In case anyone else runs into this problem, I found the cause and figured out the solution and am sharing.

The Cause

You'll run into this with Outlook for Mac 2016 and any Gmail account.  

The reason why Outlook for Mac 2016's SmartFolder behaves this way is because it is searching on every folder (as one would expect).  What I didn't consider was that Google has an Inbox folder and an All Mail folder.  When you add a "Folder" column to the view, you'll notice this.  

The Fix

To avoid the duplication, you need to update your Smart Folder search so that it excludes the All Mail folder of each Gmail account.  The image below shows my Outlook for Mac 2016 with four (4) Gmail account All Mail folders excluded.
  

If you're not sure how to do this, Click your Smart Folder (or click the upper right Search box and type something and then save to create one).  

Click Advanced and then add the following search parameters:
"Read Status->Is->Unread" 

Click + 

Set the next parameter to:
"Folder->Is Not->Choose Folder".  Once you click Choose Folder, a Window opens (titled Window) with a search field. In the search field, type in All and you'll see the All Mail folder.  Select it.

If you have more than one account, repeat this with each account. 

Click Save Search once you're done.  

Now you're Smart Folder will work if you're using Gmail.