Thank you for your post. You should still be able to find the updates for Office 365 with the settings you've currently got in place. There is one more change that I would suggest you make if you have the Office 2016 ADMX templates imported into your AD.
There is a setting called Office 365 Client Management that by default is going to block 3rd party sources from updating Office 365. Enabling this setting will allow 3rd party sources, and especially the noop.exe file used for this operation, to execute and call the Click-to-Run API module to initiate the update process. See the screenshot below for the setting.