Well I just did the following back on the 13th July:
#1 Run Outlook as an Elevated Process (i.e. as Administrator) this is so that if Outlook needed to set stuff outside the Users location (i.e. SYSTEM LOCATIONS)#2 Once opened if popup saying closed with open files, then click on NO.
#3 Disable storing the Outlook settings under Cloud storage options shown in the image below:
#4 Run Registry Editor and set (add DWORD 32-bit item with name ReopenWindowsOption if not already there) ReopenWindowsOption and set its value to 1 in the following location: Computer\HKEY_CURRENT_USER\Software\Microsoft\Office\16.0\Outlook\Preferences
#5 Close Outlook and Reboot-System just to make sure new settings are loaded up.
To be honest I think it might just be the disabling of Outlook saving its settings on the cloud that was causing this issue, but I thought I would say what I changed just in case it was a combination of what I did as a whole.
If you disable the Cloud settings save you will need to have that Registry Set!
Image of Outlook settings in the cloud:

Image of Registry Editor:

I have not gotten any more of those popups since (almost a month).
I think the issue might be linked to the remote Cloud saving of the settings which is why it would ignore what you had set in the Registry, which is why it needs that registry added when you disable the saving the settings to the cloud.