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The directory structure HAS to be the exact same. The Preferred server code in the download function ONLY swaps out the server name from the download path.
http://<preferred server>/ldlogon/patch. The <preferred server>is the only part that will change
So in answer to your question, all the preferred servers will work (NetApp Devices as well) as long as the share directory structure remains identical.
I forgot to answer, No, you do not need to keep LDLogon if you redirect the patch folder. again, like above, you just need to have the same directory structured shares across your preferred servers.