Hi Great White North and All,
Thanks your post. I updated my MS Outlook 2016 last night re the first update version noted above, Version 2307 / Build 16626.20132 and again today, update to Version 2307 / Build 16626.20134.
I subsequently re-ticked my previous work around, that is ticked "Store my Outlook Settings in the Cloud" checkbox at File | Options | General | Cloud Storage Options to see if the issue of the pop-up was resolved. Initially for 10 minutes Yes, no immediate pop-ups, which has been usual since update ver2306 since back in June!, after re-ticking/selecting (Store My Oulook settings etc) - BUT alas - it didn't take long for the pop up to appear again. Quite quickly. And, as you have noted no options in the Start Up dropdown, as yet.
Thus from my perspective there has been no proper fix resulting from these updates for this thread issue at all (aside from the work arounds) resulting it appears from or since the June update! We still await the issue to be resolved by Microsoft.
Suffice to say I have left the 'Store settings to Cloud Storage option unticked and no pop-up.
For the average user of ''the product/s/versions'- I do not believe Microsoft should expect users to fiddle with their registry.
An update specific to the issue should be undertaken for its resolution. And, at least in meantime further advice from M/soft that it IS being attended to.
Cheers All.