VPP app Overridden by patch Policy

Using Microsoft Word for example. VPP version is 16.29.19090802, Patch Policy version is 16.29.19091700. We are in a transition to VPP apps so about half the population has VPP currently. What keeps the Patch Policy from updating the VPP apps to the seemingly more current non VPP version. I would assume only scope? Creating smart groups to identify the version difference seems tedious in the long term. Best practice here or just general we do it this way. I would hate for all of the VPP versions to just get over written by the patch policy.