Hey Ryan,
Am I right in assuming I could use the method described in (http://www.wyday.com/wybuild/help/automatic-updates/windows-services-console-apps.php) for updating console apps to silently update the app with no user interaction and importantly no GUI popups at all?
Correct. We also cover this topic in detail (going over various method) in the How can I completely hide the updater (wyUpdate)? faw question.
But if you want absolutely no UI and no interaction (2 separate concepts, I should note) then using the AutomaticUpdater in a service or using wyUpdate in a service is the way to go.