Less than 24 hours after releasing macOS Sierra 10.12.3 update, Apple has today pushed out a silent update which brings Gatekeeper Configuration Data to version 108, presumably for both macOS Sierra and OS X El Capitan.
As this is stored in a database, and Apple does not provide any information about these updates, I have no idea what this changes.
Anyone who now applies the Sierra 10.12.3 Combo update will need to ensure that they force fresh security updates immediately afterwards, or that Mac may continue to use version 107 of the Gatekeeper Configuration Data for many hours or days afterwards.