I kept trying the solution mentioned by J Track with no avail, yet after long trial and errors I was finally able to have the checkbox reappear by trying to edit the Universal Access plist then opening System Preferences (preferably from the dock):
plutil -replace closeViewDFRZoomEnabled -bool false ~/Library/Preferences/com.apple.universalaccess.plist
Strangely, even though the command should set this property as false, I found the property still checked in the UI, but at least I was able to turn it off again. (possibly due to combination of notes 2 and 3).
Note 1: You can view the zoom-related properties in the plist file using
plutil -p ~/Library/Preferences/com.apple.universalaccess.plist | grep -i zoom
Note 2: Give 2-3 seconds between each step.
Note 3: If the above method doesn't work you may try to kill any instances of the
cfprefsd as this comment suggests.
Note 4: I suspected the closeViewDFRZoomEnabled may be the right property by changing the TouchBar zoom level and watching the value closeViewDFRZoomLevel change.
Note 5: Tested on macOS Sierra 10.12.3