I've been having issues with geofence direct connect notifications for a while now, but only on one of our two iPhone 6's (both on iOS 9.1; all settings identical).
I just ran through the troubleshooting steps you list and upon re-install of Mobilinc on the problem phone, it's not listed on the Notifications settings in IOS. It is available in the Main Setting's view, just not in the Notifications tab. This issue did not exist prior to removing.
I'm hesitant to remove and repeat incase there is something in the settings that may assist in troubleshooting.