Question: What Should Be Done About the Discrepancies Between Local Group Policy Editor and the Registry Settings?
Solution: Nothing. To open the Local Group Policy Editor in Windows Server 2012, either go to PowerShell and type "gpedit.msc" with not quotes or without PowerShell go to the Windows button on the desktop and go to the search field. Search for "gpedit" with no quotes. Click on the result (usually just one). This will allow you to navigate through many local server settings including how and when the WSUS server on the network is reached for operating system updates.
To open the registry in Windows Server 2012, go to the Windows button on the desktop and go to the search field. Search for "regedit" with no quotes. Click on the result (usually just one). This will allow you to navigate through the local server settings.
You may find discrepancies between the settings. The registry may have hexadecimal or decimal values that are not readable to the uninitiated. Using google you can find what the otherwise cryptic settings do (e.g., what a given value for a given setting means). The apparent difference between the settings between the registry and the Local Group Policy Editor can be the result of numerous things (such as a CM tool governing the Windows Server or a PowerShell script making registry changes to the server). The inconsistencies, while a problem to systems administrators and other humans, are not a real problem. There is nothing that can be done about many of the discrepancies. The registry settings override the settings found in Local Group Policy Editor. A downside to Microsoft technologies is the occasional confusing situation like this one.
Update as of February 9th 2017: If you Google for "how do you download big files using powershell", the first overall result is a broken link. Hopefully Google will fix their results.