Obviously, with Outlook 2016, there cannot be more than one instance of Outlook. Maybe there is an option in the windows registry to retrieve the old behavior.
The problem of the Sys.OleObject() and solution recipe for Excel can be found here: https://smartbear-cc.force.com/portal/KbArticleViewer?name=Get-COM-reference-for-a-running-Excel-ins...
Hopefully, you will be able to find similar objects for Outlook and implement the same approach for it.
If you do, I think that a lot of people will appreciate it if you mention your findings here...
The solution I came up with is to look to see if outlook is running and if it is close it before making the connection. So far this seems to work.
var OutLookProcess = Sys.WaitProcess("outlook",2000);
aqUtils.Delay(2000);//Give time to close Outlook
var OutlookApplication = Sys.OleObject("Outlook.Application");