This is an UPDATE to a previous post “Outlook 2016 Can’t Create linked Mailbox Profile — Outlook 2016 Authentication Changes Impact Profile Creation“
It is beginning to look like this is not a just a linked mailbox issue. The traces seem to show that Outlook is simply not attempting to authenticate on it’s own at all regardless of the fact that it is a domain joined computer with an an authenticated user logged in.
This does not seem to be a pass-through issue. It happens on Windows 7 as well as Windows 10 so it does not seem to be an operating system issue either it is specific to Outlook 2016.
Because the prompt is based on the email address, a regular mailbox, the user will be successful without changing the ID but it still means a login prompt will occur where in Outlook 2013, the login and profile creation all happened automatically and the mailbox just opened.
In Outlook 2016, at least one login is required followed by a message to restart outlook (similar to the message a user gets when their mailbox has been moved). This may just be ‘as designed’ behavior but Microsoft has not said that yet. If so it is still an change that impacts user experience and support.