You download the original first release msi, then create a new folder and apply the patch to the msi, then create a transform file for the customized settings. Then push the new patched msi with the transform file using pdq inventory.
You can also use pdq inventory to clean up old versions of adobe reader that may cause issues. You can use the remote command tool and use the switches to silently remove only reader and leave acrobat alone. I have used this to clean up the mess that is moving from XI to DC. Ugh. Sometimes GPO fails due to some DLLs not being flagged for update or install. It is when I review the event log that i see these on the workstation. You then have to use the cleaner tool.